The county was established on February 4, 1864, with its county seat at Idaho City. It was named for the Boise River, which was named by French-Canadian explorers and trappers for the great variety of trees growing along its banks in the lower desert valley. The county is one of four Idaho counties that also existed under Washington Territory. On January 12, 1863, The Washington territorial legislature established the county containing most of Idaho below 114° 30', excluding the territory lying west of the Payette River. They established its county seat at what later became Idaho City.