The territory was officially organized on March 3, 1863, by Act of Congress,[1] and signed into law by President Abraham Lincoln.

Most of the area east of the Continental Divide had been part of the loosely defined Dakota Territory ending along the 49th parallel—now the border with Canada, then a colonial possession of Great Britain.

[4] The upheaval caused by the Civil War and Reconstruction was a distant concern to those in the comparatively stable Idaho Territory, a situation which in turn encouraged settlement.

In the late 1860s, Idaho Territory became a destination for displaced Southern Democrats who fought for the Confederate States of America during the Civil War.

The political infighting became particularly vicious in 1867 when Governor David W. Ballard asked for protection from federal troops stationed at Fort Boise against the territorial legislature.

The discovery of gold, silver and other valuable natural resources throughout Idaho beginning in the 1860s, as well as the completion of the Transcontinental Railroad in 1869, brought many new people to the territory, including Chinese laborers who came to work the mines.

By 1882, notable and powerful Idahoans successfully disenfranchised members of the Church of Jesus Christ of Latter-day Saints voters in Idaho Territory, citing their illegal practice of polygamy.

Idaho was able to achieve statehood some six years before Utah, a territory which had a larger population and had been settled longer, but was majority members of the Church of Jesus Christ of Latter-day Saints with voting polygamists.

On March 1, 1887 Congress sent a bill to President Grover Cleveland which would have returned northern Idaho to Washington Territory.

Cleveland, likely as a favor to Governor Edward A. Stevenson, refused to sign the bill and it was pocket vetoed when the session of Congress ended two days later.