The sibling cyprinid fishes Notropis cornutus and N. chrysocephalus are sympatric and appear to hybridize extensively in the lower Great Lakes region and upper Ohio River drainage. Principal components analysis of morphological characters was used to identify the parental taxa and hybrids. Starch gel electrophoresis was used to determine if these two species are reproductively isolated. Two fixed electrophoretic differences were used as genetic markers along with morphological differences to identify hybrids. Electrophoresis revealed low levels of hybridization with backcrossing in all sympatric populations, but the extent of hybridization was highly variable. Statistical analyses revealed significant deficiencies of heterozygotes in all populations where sample sizes were large enough to detect moderate deviations from Hardy-Weinberg equilibrium. F-statistic analysis indicated that N. cornutus and N. chrysocephalus are separate species because they have separate gene pools. Although reproductive isolation is imperfect, the evidence presented here supports recognition of N. cornutus and N. chrysocephalus as distinct species.