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Early history
Anatomically modern human hunter-gatherer migration into Southeast Asia before 50,000 years ago has been confirmed by the combined fossil record of the region. These immigrants might have, to a certain extent, merged and reproduced with members of the archaic population of Homo erectus, as the fossil discoveries in the Tam Pa Ling Cave suggest. Data analysis of stone tool assemblages and fossil discoveries from Indonesia, Southern China, the Philippines, Sri Lanka and more recently Cambodia and Malaysia has established Homo erectus migration routes and episodes of presence as early as 120,000 years ago and even older isolated finds date back 1.8 Million years. Java Man (Homo erectus erectus) and Homo floresiensis attest for a sustained regional presence and isolation, long enough for notable diversification of the specie's specifics.

Ocean drops of up to 120 m below the present level during Pleistocene glacial periods opened the vast lowlands known as Sundaland, enabling hunter-gatherer populations to freely access insular Southeast Asia via extensive terrestrial corridors. Modern human presence in the Niah cave on East Malaysia dates back to 40,000 years BP, although archaeological documentation of the early settlement period suggests only brief occupation phases. However, author Charles Higham argues that, despite glacial periods modern humans were able to cross the sea barrier beyond Java and Timor, who around 45,000 years ago left traces in the Ivane Valley in eastern New Guinea "at an altitude of 2000 m exploiting yams and pandanus, hunting, and making stone tools between 43,000 and 49,000 years ago."

Signs of an early tradition are discernible in the Hoabinhian, the name given to an industry and cultural continuity of stone tools and flaked cobble artifacts that appears around 10,000 BP in caves and rock shelters first described in Hòa Bình, Vietnam, later also documented in Terengganu, Malaysia, Sumatra, Thailand, Laos, Myanmar, Cambodia and Yunnan, southern China. Research emphasizes considerable variations in quality and nature of the artifacts, influenced by region-specific environmental conditions and proximity and access to local resources. Remarkable is nonetheless that the Hoabinhian culture accounts for the first verified ritual burials.

Neolithic migrations
The earliest Homo sapiens immigrants, loosely identified as Australo-Melanesians, Aboriginal, Negritos and Hill Tribes are associated with the occupation of caves, rock shelters and isolated upland regions in Vietnam, Thailand and the Philippines or on remote islands, such as the Andaman Islands and although displaced from the coasts and plains they are present in all regions for at least 30,000 years.

Subsequent Neolithic immigration waves are intensely debated considered dynamic and complex, and research has resorted to linguistic terms and argumentation for group identification and classification. Genetics as a research tool has been established only recently but results tend to contradict conventional theories.

The Austroasiatic migration wave centered around the Mon and the Khmer, who originate in North-Eastern India arrive around 5000 BP and are identified with the settlement on the broad riverine floodplains of Burma, Indochina and Malaysia.

The origin, period and settlement pattern of the Austronesian immigrants, whose elusive branches would eventually be dispersed all over the islands between Madagascar and Oceania, has been for a long time interpreted on a linguistic basis, although more recent genetic research contradicts these ideas. Certain is, these marine migrants were accomplished seafarers, who arrived on boats around 4,000 BP and soon dominated maritime Southeast Asia, populated the lowlands and coasts and pushed indigenous people of Indonesia, the Philippines or New Guinea to the interior regions.

Two layer hypothesis
Between around 1,700 and 1,000 BC people settled in the Southeast Asian lowlands as wet-rice and millet farming techniques from the Yangtze River valley were adopted. Author and archaeologist Charles Higham suggests in his work "Hunter-Gatherers in Southeast Asia: From Prehistory to the Present" "the indigenous hunter-gatherers integrated with intrusive Neolithic communities and, while losing their cultural identity, contributed their genes to the present population of Southeast Asia." or alternatively the "hunter-gatherers withdrew to rainforest refugia and, through selective pressures inherent in such an environment, survived as the small-bodied, dark-skinned humans found to this day in the Philippines, Peninsular Malaysia and Thailand, and the Andaman Islands." Unfortunately the Two layer hypothesis, based on the human occupation of mainland Southeast Asia during two distinct periods by two separate racial groups is only applicable when you know who really was involved in this integration process. Immigration from China alongside the introduction of farming occurred and DNA testing calls for revision of Neolithic migrations.

Cambodia was inhabited during the second and first millennia BC by a Neolithic hunter and gatherer culture that may have migrated from southeastern China to the Indochinese Peninsula, responsible for the construction of circular earthworks.

Bronze Age (1000–500 BC)

 * Bronze Age, mainland Southeast Asia, ca. 1500 B.C.–500 A.D
 * Bronze and Iron Age, island Southeast Asia, ca. 1000 B.C.–500 A.D

The Iron Age period beginning around 500 BC, the inhabitants had developed complex, organised societies and a varied religious cosmology by the 1st century CE and engaging in maritime trade, resulting in socio-political interaction with the Indosphere. These original inhabitants spoke advanced Austroasiatic languages and participated in the exchange of contemporary technologies.

Islam in Maritime Southeast Asia
From the 8th century onward the coastal trade and shipping of India came to be increasingly controlled by Muslims from such regions as Gujarat

and various parts of south India, elements of Islamic culture began to filter into island Southeast Asia.

The islands had been in contact with Islam, through Arab traders, for many centuries; but their traditional cultural dependence on India prevented Islam from being acceptable to them until Islam was firmly established under Moslem rulers in the north of India itself

But only in the 13th century after the collapse of the far-flung trading empire of Shrivijaya, which was centered on the Straits of Malacca between Malaya and the north tip of Sumatra, was the way open for the widespread proselytization of Islam.

Islam spread in Southeast Asia via Muslims of diverse ethnic and cultural origins, from Middle Easterners, Arabs and Persians, to Indians, and even Chinese, all of whom followed the great commercial routes of the epoch. Islam — a cultural element amongst others — was thus part of the vast tide of exchange, treading the same path as Hinduism and Buddhism centuries before.

With its great war fleets, Shrivijaya controlled trade in much of the area and was at times so powerful that it could launch attacks on rival empires in south India. Indian traders, Muslim or otherwise, were welcome to trade in the chain of ports controlled by Shrivijaya. Since the rulers and officials of Shrivijaya were devout Buddhists, however, there was little incentive for the traders and sailors of Southeast Asian ports to convert to Islam, the religion of growing numbers of the merchants and sailors from India. With the fall of Shrivijaya, the way was open for the establishment of Muslim trading centers and efforts to preach the faith to the coastal peoples. Muslim conquests in areas such as Gujarat and Bengal, which separated Southeast Asia from Buddhist centers in India from the 11th century onward, also played a role in opening the way for Muslim conversion.

On the Relationship between Cheng Ho and Islam in Southeast Asia

The Rise of Chinese Mercantile Power in Maritime Southeast Asia, c. 1400–1700

Buddhism
EXPANSION OF BUDDHISM INTO SOUTHEAST ASIA

Early relations with China
Earliest attested trading contacts existed between Southeast Asia and the Chinese Shang dynasty (around 1600 BCE to around 1046 BCE), when cowry shells served as currency. Various natural products, such as ivory, rhinoceros horn, tortoise shells, pearls and birds’ feathers found their way to Luoyang the capital of the Zhou dynasty, that lasted from 1050 to 771 BCE. Although knowledge about port localities and shipping lanes is very limited, it is assumed that most of this exchange took place on land routes and only a small percentage was shipped "on coastal vessels crewed by Malay and Yue traders".

Military conquests during the short lived Han dynasty (221 to 206 BCE) brought a number of foreign peoples within the Chinese empire when the Imperial Chinese tributary system began to evolve under Han rule. This tributary system was based on the Chinese worldview, that had developed under the Shang dynasty, in which China is deemed the center and apogee of culture and civilization, the Middle kingdom (Zhōngguó), surrounded by layers of increasingly barbarous peoples. Contact with Southeast Asia steadily increased by the end of the Han period.

from 1069 onwards, economic and fiscal reforms were promulgated for the purpose of expanding and monetizing Chinese economic activities. In addition to establishing these maritime trade offices, the Song state also actively encouraged foreign maritime traders to come to the Chinese ports. In 987, four missions were sent with imperial credentials to encourage “foreign traders of the Southern Ocean and those who went to foreign lands beyond the seas to trade” to come to the southern Chinese ports in order to obtain preferential licenses. in 1074, a ban on the export of copper coins, which had been instituted in 960, was lifted to further encourage maritime trade. This resulted in massive exports of copper coins to Southeast Asia.

By the late 11 th century, envoys to Song China were paid for their goods in copper coin and silver bullion, and no longer in the gold, silver or copper objects previously provided. 35 Such payments/rewards were provided to, for example, missions from Champa (1072 and 1086), an Arab polity (1073), the Chola polity (1077), and Srivijaya (1078).

In 1127, the first year of the new administration, the export of copper coins was banned, and at the same time, the emperor declared that foreign goods constituted an unnecessary luxury. Thus quotas were instituted for goods imported from the South Seas. 37 This ban on export of copper coins was repeated in 1133. Foreign traders coming to the Song were still paid in copper cash, but they were expected to convert their cash into other Chinese products before leaving.