The helminth fauna of the bolson pupfish Cyprinodon atrorus (Osteichthyes: Cyprinodontidae) consisted of 7 helminth taxa collected from 7 localities of Cuatro Ciénegas, a natural area protected by the Mexican government in Coahuila, northern Mexico. The helminth community is described at the infracommunity and component community levels. The acanthoeephalan Atactorhynchus duranguensis was the most prevalent and abundant species. The remaining species were rare and found at low mean abundance values. The observed species richness, individual parasite abundance, and diversity were low at both component community and infracommunity levels. These findings are similar to those found in other freshwater fish species in the Nearctic part of Mexico; however, our study shows that the number of larval forms, in terms of species richness and abundance, is very low in comparison with previous studies in the area. Isolation of the Cuatro Ciénegas basin from the Bravo River (= Grande River) basins is suggested as the main factor determining the depauperate helminth assemblage. The low number of individual larval stages in this fish species is probably due to the lack of piscivorous birds in the area.