Robert Lee Hatcher discovered and staked the first lode gold claim in the Willow Creek Valley in September 1906, and others soon followed. But lode mining was expensive for an individual operator; it required elaborate tunnels and heavy equipment, so companies merged to pool resources and reduce expenses.

What is now called Independence Mine was once two mines: The Alaska Free Gold (Martin) Mine on Skyscraper Mountain, and Independence Mine on Granite Mountain. In 1938 the two were bought together under one company, the Alaska-Pacific Consolidated Mining Company (APC).

By 1942, the United States had entered World War II, and the War Production Board designated gold mining as nonessential to the war effort. Gold mining throughout the United States came to a halt, but Independence Mine continued to operate because of the presence of sheelite. Sheelite occurs in some of the quartz veins along with gold, and was a source of tungsten, a strategic metal.

In 1974, Independence Mine was entered into the National Register of Historic Places