We estimated genetic diversity in cave (hypogean) and surface (epigean) populations of the Mexican Tetra, Astyanax mexicanus, using RAPDs and microsatellites. By either measure, genetic diversity was significantly lower in hypogean than in epigean populations, although there was considerable variability in both classes. We examined three factors potentially influencing genetic diversity among hypogean populations: relative population size, cave isolation, and the presence of eyed fish in the cave. Of the three, only the presence of epigean forms within the caves correlated with increased genetic diversity in cave populations. This suggests that increased genetic diversity of A. mexicanus cave populations reflects introgression of alleles from surface populations. Estimation of migration rates among populations using microsatellites supported this conclusion and also suggested that alleles can move among cave and surface populations more easily than from cave to cave.