An allozyme survey of thirty-four loci from seventeen populations of the goodeid fish Goodea atripinnis was conducted to examine the extent of differentiation between continuous and isolated populations. Differentiation, based upon the Rogers genetic distance, among a group of populations isolated since the Pleistocene was no greater than that observed among apparently continuous populations within a single lake/river system. These data suggest that, for Goodea, the presence or absence of gene flow (the physical contiguity of the populations) is a minor factor in determining the extent of genetic differentiation.