We examined the relationships between two hatchery and two wild populations of the endangered Colorado squawfishPtychocheilus luciusby use of starch gel electrophoresis of 44 presumptive locus products. Samples of fish from the Green and Colorado rivers were found to be very similar to two hatchery stocks established in 1973 and 1978 (unbiased genetic identity = 0.99; Nei 1978). At least 9 of the 44 loci were polymorphic. Average heterozygosities were high (2.6–5.3%) for an endangered species but were similar to those for nine other cyprinid genera. The proportion of polymorphic loci ranged from 9.1 to 13.6%, which was also high when compared with reported values of 4% for a congener. Genotypes deviated from Hardy–Weinberg proportions at two loci (EST-1*,GPI-2*) in the Colorado River samples and at one locus (EST-1*) in the Green River samples. Also, as a secondary objective we resolved five of the nine polymorphic loci from samples of fin tissue.