Pupfish are also confused with the closely related live-bearer family of fish, which includes mosquito fish, mollies and guppies. The desert pupfish is a small, deep-bodied fish that may reach a length of about three inches. Males are usually larger and stouter than females. Mature males in breeding coloration are bright blue, with lemon yellow tails. The tail fin has a dark terminal band.
Females are tan to olive, with disrupted vertical bars along the sides.
These bars are not as prominent in males. Historically, the desert pupfish inhabited springs, slow-moving streams, rivers, and seeps in Arizona, California, Baja California, and Sonora, Mexico. The desert pupfish once occupied a much larger area that today is known as the lower Colorado River and Salton Sink, in Imperial and Riverside counties. Further isolation of the desert pupfish occurred when the present Salton Sea was formed. From 1905 to 1907 a break in a levee in the Imperial Valley allowed enormous quantities of Gila and Colorado River water to flood the Salton Basin.