Thirteen natural populations of R. cataractae were surveyed for genic variation at 21 loci yielding a mean estimate of heterozygosity (0.054) similar to heterozygosity values for vertebrates in general. Northsouth clines in heterozygosity and Est-1 gene frequencies were noted in the Connecticut River system. Evidence was presented which indicated that these clines resulted from drift and founder effect and that random processes were the primary determinants of gene frequency in southern Connecticut River populations of R. cataractae. Most protein polymorphism in similar headwater fish species probably represents effectively neutral variation in the sense that gene frequencies in many populations are determined primarily by stochastic, not deterministic, processes.