Two species of minnows, Cyprinella lutrensis (Notropis) and C. umbratilis (Cyprinidae) were sampled from Denton and Hickory Creeks, respectively, in northcentral Texas during periods of continuous flow and intermittency from 1983 to 1986. Allozyme variability was assessed for 14 structural loci in each species. Average heterozygosity (H) in C. lutrensis ranged from 0.10 to 0.16, and proportion of polymorphic loci (P) ranged from 0.44 to 0.78, while H and P in C. umbratilis ranged from 0.00 to 0.08 and 0.00 to 0.44, respectively. Heterozygote deficiencies were observed during flowing and intermittent conditions for both species, accounting for deviations from Hardy-Weinberg equilibrium. Temporal heterogeneity, measured by Fs-r, was higher in C. lutrensis (0.403) than in C. umbratilis (0.121). Allele frequencies fluctuated significantly in C. lutrensis but not in C. umbratilis. Genetic similarities between populations of C. lutrensis from flowing and intermittent conditions were highest between intermittent and subsequent flowing events. It is likely that intermittency resulted in a bottleneck and genetic drift, restructuring the genome of these fish as colonizers for subsequent flowing populations. These effects were less pronounced in C. umbratilis. Alternate effects ofintermittency on the genomes of the species reflect differences in genetic strategies of a generalist, C. lutrensis, and a relative specialist, C. umbratilis.