The pygmy whitefish is found mostly in the northern Rocky Mountains, with three other disjunct populations. One is in Lake Superior, another is in southwestern Alaska, and the third is in the Ekityki Lake, Chukchi Peninsula, Russia. The pygmy whitefish's range probably was continuous until the late Pleistocene. In the Rocky Mountains it is found in cold and rapid streams, and in cool lakes at depths of over . In Lake Superior it is found in cooler water, at depths of .