At the end of the last ice-age boulders and clay moraine blocked off a tributary of the headwaters of the Arkansas River in what is now the state of Colorado.

Recent research has speculated that the yellowfin cutthroat may have been native to the entire Arkansas River basin, not just Twin Lakes.

In July 1889, Professor David Starr Jordan and G. R. Fisher visited Twin Lakes and published their discoveries in the 1891 Bulletin of the United States Fish Commission.

In the species description, published in the 1890 edition of the Proceedings of the United States National Museum,[3] Jordan and Evermann described the fish as follows: Color, silvery olive; a broad lemon yellow shade along the sides, lower fins bright golden yellow in life, no red anywhere except the deep red dash on each side of the throat.

[4] Until about 1903, greenback and yellowfin cutthroats survived together in Twin Lakes, the populations remaining isolated as both breeders and feeders.