Native trout populations throughout western North America have declined because of habitat alteration, introgression with introduced trout, or competitive exclusion by nonnative species. Consequently, identification and preservation of native trout are now the goals of many management programs. We examined allozyme and mitochondrial DNA (mtDNA) variation in seven naturally occurring populations and one hatchery population of rainbow troutOncorhynchus mykissfrom southern Idaho and northern Nevada to determine their genetic origins. Allozyme and mtDNA results were concordant in identifying three populations as genetically pure interior rainbow trout and one population as a hybrid swarm. Results for the remaining four populations were discordant. However, these latter four populations were best classified as hybrid swarms due to the nature of either the allozyme or mtDNA data, which included genetic characteristics of both coastal and interior rainbow trout. Our study demonstrates the utility of mtDNA analysis in conjunction with independent criteria such as allozymes for detecting hybridization at the population level. Hybridized populations exhibited a greater number of mtDNA haplotypes than did genetically pure populations. Haplotypes within hybridized populations differed more from one another than did mtDNA haplotypes within nonhybridized populations.