We estimated the amount of genetic divergence among seven cutthroat trout Salmo clarki subspecies and rainbow trout Salmo gairdneri using electrophoretic data from 46 protein loci. There was little genetic divergence among the Colorado River, finespotted, greenback, and Yellowstone subspecies of cutthroat trout, but a large amount existed among the coastal, Lahontan, and westslope subspecies. These latter three subspecies were electrophoretically as similar to rainbow trout—or more so—as they were to the other four subspecies of cutthroat trout examined. Morphologically, in contrast, the cutthroat trout subspecies were all more similar to each other than to rainbow trout. The data, therefore, suggest that morphological and protein evolution have proceeded at different rates among some of these fishes. The presence of fixed or nearly fixed allele-frequency differences between the subspecies of cutthroat trout and rainbow trout and between many pairs of cutthroat trout subspecies provides a powerful means of identifying “genetically pure” populations of these taxa.