We determined variability in counts of meristic features (pyloric caceae, vertebrae, pelvic fin rays, gill-rakers, basibranchial teeth, scales above the lateral line, and scales in the lateral series) of Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri) by 3 independent readers, by the same reader on 3 different occasions, and among fish from 12 sampling sites within a 650-km2 watershed. Genetic purity of the cutthroat trout was determined by electrophoretic analysis. Significant differences in meristic counts were observed among 3 readers and among sampling sites, but not among 3 occasions by a single reader. Scale counts were within the reported range for Yellowstone cutthroat trout, but counts of other structures (pyloric caceae, gillrakers, vertebrae) were as similar to rainbow trout as to Yellowstone cutthroat trout. Meristic counts identified the fish as cutthroat trout; however, variation among readers and sampling sites as well as within the species, limits their use when identifying genetically pure cutthroat trout or assessing possible integration with rainbow trout.