Putumayo genocide

The Putumayo genocide (genocidio del Putumayo) refers to the severe exploitation and ethnocide of the indigenous population in the Amazon rainforest during the Amazon rubber boom (1879-1912). Perpetrated primarily by the Peruvian Amazon Company, led by Julio César Arana, the genocide involved extreme violence, enslavement, and inhumane conditions inflicted upon the indigenous people in pursuit of rubber extraction. The genocide began with the exploration and settlement of uncolonized land in the Amazon by various South American countries, which led to the subjugation of local tribes.

Arana's company, initially a partnership with Benjamín Larrañaga, expanded its operations by enslaving the native population and subjecting them to brutal violence. The Peruvian Amazon Company became notorious for its cruel treatment of the indigenous people, forcing them to work under inhuman conditions that often resulted in death or severe punishment. The company trained a group of indigenous males, known as  Muchachos de Confianza  ("boys of trust"), to act as enforcers and torturers against their own people. Key figures in the company, including Elías Martinengui, Andrés O'Donnell, and the Rodríguez brothers, were implicated in widespread starvation, torture, and killings.

The Putumayo genocide resulted in the annihilation of 90% of the affected Amazonian populations. Despite the issuance of 215 arrest warrants against employees of the Peruvian Amazon Company in 1911, the company continued its operations, further exploiting and abusing the indigenous population. Even after the company's liquidation, Arana and his associates retained control over the indigenous population in the Putumayo region, leading to forced relocations and continued exploitation. Although the genocide holds significant historical importance, it remains relatively unknown. Witness accounts by individuals such as and Roger Casement brought global attention to the severe conditions and abuses faced by the indigenous people.

Background
The Cinchona boom and the beginning of the Amazon rubber boom in 1879 encouraged exploration and settlement of uncolonized land between Brazil, Colombia, Peru, and Bolivia. Rafael Reyes carried out one of the first main expeditions in the Putumayo River basin in 1874 in search of Cinchona pubescens, a plant that produces quinine.{{efn|Prior to the rubber boom, Cinchona and Smilax officinalis (Sarsapilla} were the most-profitable extractive industries in the Amazonian basins of Colombia and Peru. Sarsapilla can be used as a treatment for psoriasis, and quinine was a treatment for malaria and yellow fever.}} Reyes operated in the Putumayo between 1874 and 1884, and stationed his headquarters at La Sofia, which was the furthest point of navigation for steamboats on the Upper Putumayo River. Members of this expedition later returned to the region, noting the abundance of rubber trees and indigenous tribes to potentially use as a workforce. Between 1884 and 1895, a wave of new people sought to exploit these resources; these people included Calderón Hermanos, Crisóstomo Hernández, and Benjamin Larrañaga, the latter two being Colombians and veterans of Reyes' 1874 expedition

Benjamin Larrañaga and Hernández set up operations on the Igara Paraná River at a settlement that became known as La Chorrera. A group of Colombians led by Rafael Tobar, Aquiléo Torres, and Cecilio Plata initiated a campaign of conquest against natives in the areas that later became known as Entre Rios, Atenas, and La Sabana. Afterwards, Gregorio Calderon and one of the Larrañaga's led an expedition towards the Cara Paraná River; they began another conquest to enslave the natives around El Encanto. These men decided to exploit the Huitotos, the Andokes, and the Boras tribes into debt or enslavement with the goal of extracting rubber. According to Roger Casement in 1913:

"The foundations thus laid by Crisostomo Hernandez and Larrañaga in 1886 grew, not without bloodshed and many killings of the Indians, into a widespread series of Colombian settlements along the banks of the Caraparaná and Igaraparana, and even in the country stretching between the latter river and the Japura and on the upper waters of the Cahuinari."

Joaquin Rocha, a Colombian who travelled through the Putumayo region, said by 1897, Crisóstomo Hernández had subdued the entire Caraparaná region and a large portion of the Igaraparana River. Hernández waged war against the tribes that would not work or trade with him; during these conflicts, Hernandez acquired aid from tribes he had previously entrapped. In his 1905 book, Rocha provided an eyewitness account of a massacre that was relayed to him by an ex-employee of Hernandez. This source stated Hernandez ordered his employees to exterminate a tribe of Huitotos known as the Uruhuai, including the men, women and children, because they were rumoured to have practised cannibalism. Hernandez was later killed in an accident while one of his employees was handing him a loaded rifle. In his 1991 book, anthropologist Michael Taussig examined the history and conditions that led to the Putumayo genocide, and Peruvian anthropologist Alberto Chirif noted Taussig's examination of Crisostomo Hernandez "demonstrates that the massacres against the indigenous people in the Putumayo were already taking place before [Julio César] Arana's arrival".



In 1896, Julio César Arana expanded his small peddling business in Iquitos and began to trade with Colombians in the region. At the time, it was easier for the Colombians to secure supplies from Iquitos rather than from Colombian territory. A year later, Arana's most-successful competitors in Peru Carlos Fitzcarrald and Antonio de Vaca Diez died in a boating accident in the Urubamba River. Along with the Putumayo, the basins of the Urubamba and the Madre de Dios were the biggest producers of rubber in Peru. After the collapse of the Fitzcarrald's and Vaca Diez' enterprises and their partnership with Nícolas Suarez, the Putumayo became the most-significant rubber-producing region of Peru.

Arana entered a partnership with Benjamin Larrañaga, forming Larrañaga, Arana y compañia in 1902. After Larrañaga's death on December 21, 1903, Arana bought out Rafael Larrañaga's share of the company, "taking advantage of their ignorance and stupidity to rob them scandalously". The Calderon brothers at El Encanto became indebted to Arana's enterprise and sold their property to Arana in July 1905. Along with the acquisition of El Encanto, there were 3,500 Huitoto natives on the estate dedicated to the extraction of rubber who became part of Arana's workforce.

By this time, Arana was the dominant force on the Igaraparaná River; he was only challenged by insignificant bands of Colombian rubber tappers and indigenous tribes who were not yet under his control. To administer his territory, the management was split between the two departments of La Chorrera and El Encanto. La Chorrera was the company headquarters along the Igara Paraná River while the headquarters for the Caraparaná River was in El Encanto. All of the subsections and rubber tappers had their products delivered to their headquarters to be exported through Iquitos.



At the hands of Arana's company, natives suffered enslavement, kidnapping, separation of families, rape, starvation, use for target practice, flagellation, immolation, dismemberment, and other extreme violence. People who were too old or no longer able to work were murdered. Most of the elderly natives were killed during the early stages of the genocide because the slavers viewed their advice as dangerous.



In 1907 after successful business meetings in England, Julio Arana formed his company into the Peruvian Amazon Company, to which the Government of Peru ceded the Amazon territories north of Loreto after the company's founder Arana purchased the land. Shortly after, private hosts of Arana – brought from Barbados – which consisted of forcing natives to work for him in exchange for "favors and protection"; the offer could not be refused because disagreements led to their kidnapping by mercenaries paid by the company. Native people were subjected to isolation in remote areas to collect rubber in inhuman conditions and were punished with death or internment in labour camps if they did not collect the required amount of rubber. Ninety percent of the affected Amazonian populations were annihilated.

The Peruvian Amazon Company
The Peruvian Amazon Rubber Company was registered in London on September 6, 1907, as a successor to J.C. Arana y Hermanos, whose assets the new company acquired. The word rubber was later removed from the Peruvian Amazon Company's name. The old company employed 196 Barbadian men in the Putumayo around 1904, many of whom became employed by the Peruvian Amazon Company. These Barbadians were British subjects.

Eugene Robuchon drafted the company prospectus and the Peruvian consul-general Carlos Rey De Castro edited it. Rey de Castro's editing process intended to portray this new company as a "civilizing force" and led to the removal of several paragraphs Robuchon wrote from the final publication. The prospectus stated there were more than forty stations delivering rubber to La Chorrera's agency and eighteen stations delivering to El Encanto. Roger Casement said: "the English Company is only English in name". In 1910, when Casement investigated the Peruvian Amazon Company books in Manaus, he found Rey de Castro had an outstanding debt of between £4,000 and £5,000 to the Peruvian Amazon Company.

In June 1911, 215 arrest warrants were issued against employees of the Peruvian Amazon Company, primarily among La Chorrera's agency. They were implicated "with a multiplicity of murders and tortures of the Indians all through that region".

Indigenous workforce
To secure their workforce, the Peruvians and Colombians initiated slave raids, during which indigenous people were either captured or killed. The slavers would bring in chiefs and their tribes, inducing them to collect rubber under the threat of death. Chiefs who refused or did not bring in enough rubber were murdered as examples. Through fear and entrapment of natives into a debt relationship, the exploiters managed a system of slavery. Some natives were recruited at a very young age to act as trusted killers for the company; these natives became known as muchachos de confianza. The Barbadians and muchachos de confianza acted as enforcers and executioners for plantation managers. They managed the collection of rubber and tribal chiefs who were allowed to live.

Exploiters would send natives into the wild forest to collect rubber. Managers working for the Peruvian Amazon Company earned a commission that was based on the amount of rubber their indigenous workers collected. A weight quota that was dictated by a manager was set for each plantation. Punishments for not meeting the quota included flagellation, immolation, dismemberment, and execution.



As well as collecting rubber for the company, natives were expected to provide food and firewood; labour for clearing paths in the forest for roads between stations, the construction of bridges and buildings, and for clearing the forest around the stations; and "every other conceivable form of demand", including giving their children or wives to company employees. Natives worked without pay for the company under threat of terrorization or death. The Amazon Journal of Roger Casement and The Putumayo, The Devil's Paradise by Walter Hardenburg include numerous mentions of starvation among the indigenous population. According to Casement:

"The trees are valueless without the Indians, who, besides getting rubber for them, do everything else these creatures need – feed them, build for them, run for them and carry for them and supply them with wives and concubines. They couldn't get this done by persuasion, so they slew and massacred and enslaved by terror, and that is the foundation. What we see today is merely the logical sequence of events – the cowed and entirely subdued Indians, reduced in numbers, hopelessly obedient, with no refuge and no retreat, and no redress."

Muchachos de Confianza
Muchachos de Confianza ("boys of trust") were a group of Indigenous males who were trained at a young age to act as killers and torturers against the native workforce. They were often employed in areas where their tribes had long-standing hostilities or were traditionally antagonistic. Muchachos de Confianza were also referred to as racionales ("rationals") a part of an imposed hierarchy that divided "semi-civilized" natives and those who were considered non-civilized. The Peruvian Amazon Company outfitted its muchachos with Winchester rifles and shotguns. Muchachos risked death if they disobeyed.



According to judge Romulo Paredes, they "place at the disposal of those chiefs their special instincts, such as sense of direction, scent, their sobriety, and their knowledge of the mountains, in order that nobody might escape their fury". According to Paredes, muchachos were often the authors of fictitious uprisings or similar rebellions. These lies were encouraged by the fact they were rewarded for their services. Roger Casement described the system as "Boras Indians murdering Huitotos and vice versa for the pleasure, or supposed profit, of their masters, who in the end turn on these (from a variety of motives) and kill them". Casement was also convinced the agency at La Chorrera did not inquire into disappearances of muchachos. According to Casement, the muchachos de confianza outnumbered Peruvian Amazon Company employees in the Putumayo by two to one. In certain areas of the Peruvian Amazon Company estate, the management of the enslaved rubber-collecting workforce was dependent on the muchachos de confianza. There were numerous cases of rebellions perpetrated by muchachos de confianza but they were all small-scale incidents. According to Casement, one of these rebellions was a representative case for the practice of grooming muchachos de confianzas:

"Incidentally, too, it illustrates the depravity entailed by the whole system. 'Chico' was one of the 'civilized' Indians of Abisinia – one of those armed and drilled to obey and execute the orders of the civilisers on the wild, or in other words, defenceless Indians. With what result? He revolts. He becomes 'a bandit', an armed terror 'threatening the lives of white men even', and so is shot out of hand by a labourer of British birth in the Company's service."

Correrias
One method for the accumulation and expansion of a native workforce by rubber extracting firms in the Putumayo, were correrias ("forays" or "chasings"). Employees of the Peruvian Amazon Company also referred to these raids as "commissions". These were hunting parties or slave raids that were sent out to either kill or capture natives. Correrias were also sent out in the event of natives running away or as a consequence of the failure of a group to collect enough rubber. Natives caught in these raids were often put in chains and then subjected to the cepo on their arrival to a rubber station. Correrias are known to have continued up to 1910, and that year at least two raids carried out across the Caqueta River. One of these expeditions was carried out by Augusto Jímenez; twenty-one natives and three Colombian men were captured. The other raid was carried out by Armando Normand, and spent at least twenty-one days away from Matanzas, six of which were spent in Colombian territory across the Caqueta. Normand's group captured six natives. Joshua Dyall, a Barbadian that was employed with Normand in 1904, reported that Normand and his fellow managers gave orders to their subordinates shoot any indigenous people that they could not capture. This was done "to frighten the Indians and make them come in, because if they were killed for running away they would be less likely to run."

Rubber stations
The Peruvian Amazon Company had dozens of plantations throughout the Putumayo region. Many of these settlements were acquired through exploitative business deals or by force, and were used as centres of control for the company against the Natives. Slave raids to secure an indigenous workforce, which would have to deliver the rubber to the nearest company station or face torture and possibly death, were carried out from the stations. Plantations usually consisted of a centralized settlement surrounded by cleared forest. Any attack against these stations would have to face open ground with no cover from bullets. In reference to the stations located further inland, Seymour Bell, who was a member of the 1910 investigatory commission, stated stations "were all really 'forts'".



Depending on the local station, natives could walk as far as 60 miles while carrying between 100 to 165 lbs of rubber. Often, these couriers were given little or no food on their journey and had to scavenge for food. The children and family of these native rubber tappers would often travel together; if not, it was likely those dependents could starve to death.

La Chorrera
La Chorrera was an important settlement along the Igaraparaná River during the rubber boom. It was initially settled by Colombian rubber exporters but had come into the possession of Julio Cesar Arana by the beginning of 1904.

Some of the first reports of the Putumayo genocide regarding the killing of 25-40 Ocaina natives originated at La Chorrera in September 1903. Two witnesses gave depositions to Benjamin Saldaña Rocca about the killings, which they stated were instigated by Rafael Larrañaga and Victor Macedo. The natives were flogged for hours, and later shot and burnt. A judge who was sent to investigate the region in 1911 later corroborated this report. On April 7, 1911, the judge issued twenty-two arrest warrants against individuals who had participated in the 1903 massacre of Ocaina natives. They were implicated with "the crime of flogging and flaying thirty Ocainas Indians and then burning them alive". Another set of warrants was issued against 215 employees of La Chorrera's agency for their perpetration of crimes against the local natives. Arana purchased the Larrañaga share of La Chorrera and assumed control over the Igaraparaná River shortly after this incident.

Sometime between 1903 and 1906, Macedo became the manager of Arana's company at La Chorrera, which operated as a regional headquarters on the Igaraparaná. In 1906, Macedo was said to have given an order to: "kill all mutilated Indians at once for the following reasons: first, because they consumed food although they could not work; and second, because it looked bad to have these mutilated wretches running about. This wise precaution of Macedo's makes it difficult to find any mutilated Indians there, in spite of the number of mutilations; for, obeying this order, the executioners kill all the Indians they mutilate, after they have suffered what they consider a sufficient space of time."

By 1907, La Chorrera's agency retained effective control over the land between the Igaraparaná and Caqueta Rivers. The stations of La Sabana, Santa Catalina, Atenas, Entre Rios, Occidente, Abisinia, Matanzas, La China, Urania, and Ultimo Retiro delivered their rubber to La Chorrera. All of these sections were reported to practice flagellation of natives, and on a number of occasions, natives died the wounds caused by the floggings. The scarification of wounds from flogging were termed the "Mark of Arana". Starvation was also used to punish natives; according to Roger Casement: "[d]eliberate starvation was again and again resorted to, but this not where it was desired merely to frighten, but where the intention was to kill. Men and women were kept prisoners in the station stocks until they died of hunger."



The stations at Abisinia and Matanzas appear most frequently in the reports of abuse collected by Walter Ernest Hardenburg. Both stations established by Arana's enterprise with the help of Barbadian men around 1904. Many of the Barbadians who were employed by the company at these stations were sent on "commissions" or slave raids. Both Matanzas and Abisinia were inland stations, which meant long marches for natives collecting rubber. Roger Casement referred to them in 1910 as "the two worst stations". Matanzas was situated near the Caqueta River and was managed by Armando Normand from 1906 to 1910. According to a 1907 report by Charles C. Eberhardt, who was the American consul in Iquitos, there were approximately 5,000 natives at Matanzas, and 1,600 at Abisinia. In 1910, Normand told Casement he had two fabricos in a year, and his station brought in around 8,500 kg for each fabrico. That year, the collection for Matanzas was done by 120 men "working" rubber who collected 140 kg a year. The Abisinia station was situated on a tributary of the Cahuinari River and was managed by Abelardo Agüero from 1905 to 1910. In 1912, it was reported 170 natives remained at Abisinia. Agüero and Normand were both said to have committed innumerable crimes against enslaved indigenous people in their district. They were both dismissed from the company in 1910. At the time, Agüero was in debt to the company for around £500 or £600, while the company owed Normand around £2,100.

Agüero rallied a group of his subordinates and his muchachos de confianza, and set fire to the native crop fields at Abisinia. They took "a large number of Indians with them" and fled the region. A dispatch from English Consul-General Lucien Jerome to the British Foreign Office in 1911 stated the trafficking of natives was carried out with the intention to sell them and to prevent them from providing evidence and testifying to any judicial commission. Jerome also reported Agüero's group destroyed a Huitoto village. In 1915, Judge Carlos A. Valcárcel implicated Normand with the destruction of the Cadanechajá, Japaja, Cadanache, Coigaro, Rosecomema, Tomecagaro, Aduije, and Tichuina tribes.

Managers like Elías Martinengui, who oversaw Atenas, forced his workers to continue day and night, allowing them no time to plant or gather food. Regarding the Atenas plantation, Roger Casement wrote: "the whole of the population of this district had been systematically starved to death by Elias Martenengui. Martenengui worked his whole district to death, and gave the Indians no time to plant or find food. They had to work rubber or be killed, and to work and die." Women at Atenas were required to "work" the rubber, which also contributed to the starvation in that area. In 1910, when Casement visited Atenas, the station was reported to have had 790 rubber workers but Alfredo Montt said he had only "about 250" and three other Peruvian Amazon Company employees under him. The muchachos de confianza oversaw the collection of rubber, and the station brought in 24 tons of rubber annually.



Andrés O'Donnell managed the station at Entre Rios, which was another important part of La Chorrera's agency. O'Donnell was first incriminated in the Putumayo genocide by Marcial Gorries, who had worked for the Peruvian Amazon Company. In a 1907 letter to Saldaña Rocca, Marcial wrote: "O'Donnell, who has not killed Indians with his own hands, but who has ordered over five hundred Indians to be killed". The cepo at Entre Rios had twenty-four holes that could restrict limbs. Natives at this station also suffered from starvation, and the journey to deliver rubber for a fabrico resulted in many deaths each year. On top of the journey from Entre Rios to La Chorrera, some of the enslaved natives lived 25 - 30 miles away. In 1910, O'Donnell told Casement he only required two fabricos from his station, and brought in around 16000 kg for each of them but the Barbadian Frederick Bishop stated this was false, and the real quantity was closer to 24000 kg every collection period.

Bishop stated he had often seen men carrying 40 - 45 kg of rubber to Puerto Peruano, from where it was taken to La Chorrera. According to the Entre Rios staff list, twenty-three employees were stationed there, which was "the local force for controlling the life and limb of every Indian in the district". While en route to Puerto Peruano, Roger Casement noted: "We passed for fully 2 hours through the once enormous clearings of the Iguarase Indians. Tizon said they had once been very numerous. There must have been hundreds of them – now none at all. All is desolation."

The Rodriguez brothers managed the stations at Santa Catalina and La Sabana between 1904 and 1910; Aurelio Rodriguez managed Santa Catalina and his brother Aristides managed La Sabana. According to Juan A. Tizon, these two were responsible for killing "hundreds of natives" and received a 50% commission on the rubber brought into their stations. Barbadian Preston Johnson worked at Santa Catalina for eighteen months, and when asked how many natives he had seen killed there he stated: "a great many". The majority of these killings were carried out because the victim had tried to run away; several others were killed because they were not collecting rubber for the company at the time. Johnson said he knew about natives dying from starvation at La Sabana but he did not know if this was also the case at Santa Catalina. At Santa Catalina, Aurelio had built a special stockade thet was referred to as a "double cepo". One part of this cepo restrained the neck and arms, while the other end of the cepo confined the ankles. The piece that restricted the ankles was adjustable, so it could fit a variety of individuals, including children. Casement stated: "Small boys were often inserted into this receptacle face downwards, and they, as well as grown-up people, women equally with men, were flogged while extended in this posture". A number of mass killings perpetrated by the Rodriguez brothers were reported in the Hardenburg depositions by Juan Rosas and Genaro Caporo.

The station at Ultimo Retiro, one of the last important stations along the Igaraparaná River, was managed by Alfredo Montt, and later Augusto Jimenez Seminario. The cepo at Ultimo Retiro was said to have nineteen holes, which were very small. After a demonstration of this cepo, a native told Roger Casement many others had been flogged and starved to death while imprisoned there. Casement later stated this device "was not intended for a place of detention, but for an instrument of torture". In 1910, there was around 25 tons of rubber delivered to La Chorrera from this station. At its height, Ultimo Retiro had 2,000 native workers on its books but by 1912, this workforce had fallen to around 200.



El Encanto


El Encanto was the most important settlement on the Caraparaná River during the rubber boom. Originally, the settlement belonged to a few Colombians who were known as the Calderon brothers. The Calderon brothers lost their property at Encanto to Arana's company and shortly after, Miguel S. Loayza became the regional manager there. An ex-employee named Carlos Soplín, who swore before a notary, believed the inspector of sections for Encantos "must have flogged over five thousand Indians during the six years he has resided in this region". Soplin also stated in his two-and-a-half months at the Monte Rico section, he witnessed the flagellation of 300 natives, who were flogged between 20 and 200 times if the punishment was intended to kill. According to Soplin, at Esmeraldas, he was witness to the flogging of over 400 natives in three-and-a-half months; these included men, women, children and the elderly, six of whom died from the floggings they received. The plantations of Monte Rico, Argelia, Esperanza, Esmeraldas Indostan, La Florida, and La Sombra delivered their product to El Encanto. Between 1906 and 1907, the population at El Encanto dropped from 2,200, to 1,500 and the explanation provided to the American consul Charles C. Eberhardt stated smallpox had killed around 700 people.

Walter Ernest Hardenburg went to the Putumayo in 1907, shortly after the Peruvian Amazon Company was registered. A group of gunmen working for Loayza arrested Hardenburg and took him to Encanto, where he witnessed the condition of the natives there. He saw people in various stages of sickness and starvation; according to Harenburg: "These poor wretches, without remedies, without food, were exposed to the burning rays of the vertical sun and the cold rains and heavy dews of early morning until death released them from their sufferings". Their dead bodies were then carried and dumped into the Caraparaná River.

In 1908, Loayza authorized attacks against the remaining Colombian enterprises along the Caraparaná River. These included the settlements of David Serrano, Ordoñez, and Martínez. Ordoñez owned a station called Remolino, which had a portage trail between the Caraparaná and Napo Rivers established on it. Serrano was an important rubber collector on the river who owed money to the Peruvian Amazon Company branch at El Encanto. This debt was used as an excuse to send a commission to Serrano's house to rob him and intimidate him to leave the region. A second commission was sent, during which Serrano and twenty-eight of his men were captured and killed. According to Hardenburg, the men's bodies were mutilated with machetes and thrown into the river. These Colombian settlements were raided, and then either captured or burnt down in 1908. In a letter dated November 29, 1908, Loayza granted the manager of La Florida authority to assume control over the native workforce that Ordoñez and Martínez had used. The natives at Serrano's settlement were also enslaved by the Peruvian Amazon Company and added to its workforce. Around 120 Peruvian soldiers were sent from Iquitos to help the Peruvian Amazon Company employees fight against the Colombians. According to Victor Macedo, by 1910, eighty of these soldiers had died, mostly around El Encanto.

Involvement of the Peruvian government and military
The Peruvian government first established a garrison on the Igaraparana River in 1902, at La Chorrera. Three statements collected by Romulo Paredes in 1911 implicated soldiers from the garrison at La Chorrera with flogging natives at that station as early as 1903, according to one of those depositions the commanding officer of the garrison at that time had personally flogged several natives of the Aymenes nation.

Around eighty-five soldiers from the Peruvian army participated in the raids against the Colombian estates of La Union and La Reserva on January 12 of 1908. The Liberal steamship had around eighty armed agents from Arana's company onboard while the Peruvian soldiers were embarked on gunboat Iquitos. The commander of Peruvian military forces in the Putumayo, Juan Pollack, issued arrest warrants against the agents of Arana's company that participated in the attacks on La Union and Reserva. Peruvian authorities managed to capture those agents, with the notablbe exception of Bartolome Zumaeta these agents were imprisoned at La Chorrera for two months. Julio César Arana, along with Carlos Rey de Castro and the prefect of Iquitos, Carlos Zapata, travelled together to La Chorrera. Roger Casement believed that "[t]his journey of Senor Arana in company with these two Peruvian officers of high rank is really the key to the whole subsequent situation." Zapata organized the release of the men imprisoned by commander Juan Pollacks orders. Arana was later implicated by British consul David Cazes, Roger Casement and two other sources with bribing prefect Zapata an amount that varies between £5,000 and £8,000 for the release of Arana's imprisoned agents.

The owner of the Colombian estate El Pensamiento perished around May of 1908 while owing money to Arana's company as well as the British consul general in Iquitos, David Cazes. Arana and Cazes were both under the belief that they had a legal claim to acquire El Pensamiento due to the debts of the previous owner. Several Huitoto natives had fled from Arana's estates in the Putumayo and they arrived at El Pensamiento around this time. According to Cazes these natives were "dreadfully scarred from flogging" an he tried to have them admitted to the courts of Iquitos for evidence in this civil matter, however the prefect "Zapata and the Court had these Indians sent away". Cazes managed to sell all of the rubber collected at El Pensamiento prior to May of 1908, when a force of Peruvian soldiers led by Amaedo Burga embarked on the warship Reqeuna and travelled towards El Pensamiento to seize the estate for Arana's company. Burga, was the commisario of the Napo River for the Peruvian government, he was also simultaneously employed by Arana's firm as an agent. An arrest warrant was issued against Cazes by the local court in Iquitos and soldiers were sent to his house, which was also the British consulate in Iquitos. Prefect Zapata delivered an ultimatum to Cazes which was to either surrender his claim on El Pensamiento and pay a £800 fee or face imprisonment. Cazes paid the £800 fee to the court of Iquitos and afterwards commisario Burga imprisoned the Huitoto natives that had fled towards El Pensamiento and he transferred them back towards Arana's estates in the Putumayo.

Walter Ernest Hardenburg wrote that during his imprisonment on Liberal, he saw the Peruvian comissario of the Putumayo River, César Lúrquin "openly taking with him to Iquitos a little Huitoto girl of some seven years, presumably to sell her as a 'servant'". Regarding Lúrquin, Hardenburg also wrote "instead of stopping on the Putumayo, travelling about there and really making efforts to suppress crime by punishing the criminals, he contented himself with visiting the region four or five times a year—always on the company's launches—stopping a week or so, collecting some children to sell, and then returning and making his 'report.'" In 1912, lieutenant Aurelio E. O'Donovan of the Peruvian army was arrested for trafficking 12 Huitoto natives onboard steamship Hamburgo, transporting them towards Iquitos. This group of 12 natives was composed of 8 males and 4 females, all between the ages of 8 and 14.

After the Peruvian Amazon Company
After the Peruvian Amazon Company was liquidated, Arana and a number of his associates retained property in the Putumayo region, and effective control of the indigenous population. An unknown number of natives were forcefully relocated to other regions of the Amazon, where they continued to extract rubber. In 1911, it was reported several of the company's employees against whom arrest warrants had been issued had escaped from the region with up to 500 natives.

In 1912, an Irish missionary named Leo Sambrook and three other men travelled to Putumayo to set up a Franciscan mission. Sambrook noted the abuses in the area continued and in 1916, he reported a rebellion had occurred at the Atenas rubber station. This rebellion consisted of 900 men, mostly Boras natives. A month later, Sambrook reported Peruvian soldiers had quelled the rebellion. The Atenas area was recaptured, the houses of natives were burnt down, and the survivors were rounded up. Researcher and author Jordan Goodman suggests that the rebellion reported by Sambrook may be the same incident as the Yarocamena uprising, which also originated at Atenas. According to Capuchin friar Gaspar de Pinell's information, an uprising against Arana's company occurred along the Igaraparaná River in 1917 and he wrote that a company of Peruvian soldiers with a machine gun suppressed the rebellion. Two examinations on the oral history of the Yarocamena rebellion were published in 1985 and 1989, the first article was titled "La rabia de Yarocamena". The second article was named "Historia oral de una maloca sitiada en el amazonas: aspectos de la rebelión de yarocamena contra la casa arana, en 1917". Gaspar de Pinell had access to a census conducted by Arana's enterprise in 1917 which stated Arana's company had 2,300 natives dedicated to the extraction of rubber on the Caraparaná River, while on the Igaraparaná there were around 6,200 dedicated to extracting rubber.

Before the Peruvian and Colombian border changed in the 1920's, Miguel S. Loayza and his brother Carlos forced the migration of at least 6,719 Putumayo natives into the Ampiyacu region of Peru. According to Miguel's brother, around half of those natives died due to disease and other factors during the journey. The surviving natives from this group continued to work for the Loayza's until the late 1950's.

In popular culture

 * The Dream of the Celt by Mario Vargas Llosa details some of Irishman Roger Casement's experiences in investigating the Putumayo genocide.
 * Terence McKenna's travelogue True Hallucinations take place in an area affected by the Putumayo genocide, and discusses the history
 * The novel The Vortex by José Eustasio Rivera is based on the events, which are portrayed through the narration of Don Clemente Silva.
 * The film Embrace of the Serpent, which was directed by Ciro Guerra, includes characters who are affected by the Putumayo genocide.