Populations of Gila trout, Salmo gilae, and Apache trout, S. apache, from New Mexico and Arizona, respectively, as well as a trout, Salmo sp., population from the Rio Mayo, Mexico, were analyzed for protein polymorphisms at 36 presumptive genetic loci using starch gel electrophoresis. These data were used: (1) to identify the genetic differentiation between these populations and rainbow trout, S. gairdneri, and cutthroat trout, S. clarki, and; (2) to evaluate purported hybridization between the native populations and introduced rainbow trout. S. gilae and S. apache were more similar to each other than either was to S. gairdneri, S. clarki, or Rio Mayo Salmo. S. gairdneri showed a greater genetic identity to S. gilae, S. apache, and Rio Mayo Salmo than did S. clarki. In eight of the nine localities inhabited by putative hybrids, no evidence of hybridization was detected. Four streams were inhabited by unhybridized S. apache and four streams inhabited by S. gairdneri. In the latter four streams, S. gairdneri has presumably replaced the native species. In one location the entire sample consisted of hybrids.