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Incorporation and growth
Boise's early growth was driven significantly by its role in supplying the nearby gold towns that sprung up in the 1860s northeast and then southwest of the town. Miners sometimes wintered in Boise and a number of early prominent businessmen were miners who settled in town in the years after the gold rush waned. By 1864 substantial agricultural production was underway on easily irrigated lands near the river and three canal companies had been incorporated. Early transportation improvements were largely a result of toll road franchises awarded by the territorial legislature starting in the 1860s. These first ran from Fort Boise to the mining centers in the Boise Basin and east to Rocky Bar and to Rattlesnake Station where they connected to the Oregon Trail.

Territorial census records from 1864 list the population of Boise as 1,658, and an act of December 12, 1864 was the first attempt by the Idaho Territorial Legislature to incorporate the city. This was rejected by voters the following March. Two more unsuccessful attempts were made to organize a city administration by election before the 1866 version of the city charter was approved by voters on January 6, 1868. The growing number of homes and businesses, for which owners wanted proper legal title, may have contributed to the eventual success of incorporation. By 1868 Boise had over 400 permanent buildings with a wide range of commercial services. 1868 also marked the formal beginning of a long advocacy for railroad connections to other Idaho communities and, just as importantly, to other growing cities in the west such as Portland, Oregon. Competing railroad and western state government interests frustrated these efforts for many years.

Boise began to earn its City of Trees nickname in this period with a popular focus on a range of tree planting projects. Thomas J. Davis planted several thousand fruit trees in 1864 and several other early businessmen either founded nurseries or orchards of their own. In the 1870s tree planting began in earnest in downtown Boise led by prominent hotels as well as businessmen and residents. In 1907 Davis donated 43 acres of his orchard property to the city for use as a park in the name of his wife Julia.

Designed by Alfred B. Mullett, the U.S. Assay Office at 210 Main Street was built in 1871 and today is a National Historic Landmark. It first began accepting gold and silver for purchase on March 2, 1872, largely eliminating the need to transport ore to the mint in San Francisco. A territorial penitentiary, now known as the Old Idaho State Penitentiary, opened the same month several miles east of town.

Boise's growth and increasing wealth in the 1870s and 1880s was not enough to secure a long-desired rail depot as proposed projects with Union Pacific and the Oregon Short Line railways were interrupted by national financial panics, geographical challenges and a desire to couple the railroad project with other infrastructure improvements. Finally, in September 1887, a short branch line connecting Boise to Nampa's main-line depot was completed.