The authors sampled for fishes at 23 historic and potential Mexican habitats of the endangered desert pupfish, Cyprinodon macularius Baird and Girard. Though pupfish were found at 11 localities, ichthyofaunas of the region were typically dominated by exotics. Desert pupfish was found at two sites from which it had been reported extirpated. One site was found to function as an extensive pupfish refugium from which other species were apparently excluded by water quality. It is concluded that the range of species has been dramatically reduced over the last century by habitat modification and introductions of exotic fishes. Probable continued habitat alterations and limited distribution and population size in natural populations, as well as limited success of reintroduction attempts, require that the species remain considered to be very much endangered