Enzyme electrophoresis and restriction fragment length polymorphism (RFLP) analysis of Anopheles pseudopunctipennis sensu lato from nine isolated populations in neotropical America confirmed previous observations that it constitutes a species complex. Electrophoretic studies showed fixed differences at two enzyme loci, glycerol dehydrogenase (Gcd) and phosphoglucomutase (Pgm), suggesting limited or no gene flow between populations from Mexico and South America. In addition, analysis of genetic distance showed two distinctive clusters, one from Mexico and the other from South America, separated at a Nei's distance level of 0.13, a value consistent in magnitude with that of other anopheline sibling species. The RFLP analysis revealed the presence of a ribosomal DNA fragment in Mexican strains that was absent in strains from South America. Two species have been identified through these studies, one provisionally named An. pseudopunctipennis A, a species from central Mexico, and the other An. pseudopunctipennis B, for the species found in the interAndean valleys and Andean slopes in regions of Peru and Bolivia. This research provides information required to elucidate the status of the different species of the An. pseudopunctipennis complex as vectors of malaria in the Americas.