AbstractThree species of cactophilicDrosophilaendemic to the Sonoran Desert of North America,D. nigrospiracula,D. pacheaandD. mettleri, experience marked differences in spatial resource availability, and the first two of these display significant differences in dispersal behaviour. We employed starch gel and cellulose acetate electrophoresis for eight allozyme loci to test for a relationship between these variables and genetic differentiation among geographical populations of each species. No evidence was found for population structure in any of the three species, populations of which were separated by geographical distances of up to 475 km. Allele frequencies for two loci,Mdh‐1andEst‐2, inD. nigrospiraculaandD. pacheawere very similar to those obtained ≈ 30 years ago by other workers, indicating that the polymorphisms are remarkably stable under the stressful and variable conditions of the desert environment. High longevity, dispersal and multiple female remating are likely to contribute to the apparent high level of gene flow in all three species.