To assess patterns of geographic variation in the wide-ranging North American catostomid genus Cycleptus, 23 specimens were obtained from six locations among four drainage systems that exit into the Gulf of Mexico. Starch gel electrophoresis was used to compare gene products of 47 loci. A contingency chi-square test showed that the 23 samples did not come from a single, random-breeding population. Tests using exact probabilities showed that all samples from within each of the four drainage systems were in agreement with Hardy-Weinberg equilibrium expectations. Pairwise combinations showed that only two of the drainages could be combined and still result in equilibrium. Three allopatric genetic units are recognized: (1) Rio Grande drainage, (2) Mississippi drainage, and (3) the Alabama plus Pascagoula drainages. All three units can be distinguished by differences in allelic composition at certain enzymatic loci, levels of heterozygosity, number of genes expressed (some genes have been silenced in these allotetraploids), and perhaps a regulatory character involving mMdhp-A¹. We propose that these units be recognized as separate species. The Mississippi drainage population would retain the name Cycleptus elongatus (Lesueur). The Gulf Coast population has recently been described as Cycleptus meridionalis Burr and Mayden. The Rio Grande population awaits further analysis of morphological and molecular variation and a formal description.