<p>Habitat loss and fragmentation has isolated many species into small geographic areas. This is especially true of stream fishes, where alteration of waterways has restricted many species to headwater tributaries, leading to low abundances and threatening loss of genetic diversity. In addition, hybridization and introgression with introduced game fishes can impact the distribution of genetic variation among native populations. To assess the effects of habitat extent and hybridization on genetic diversity in a stream dwelling fish, we conducted a study of Redband Trout (<i>Oncorhynchus mykiss gairdneri</i>) populations within the southernmost drainages of the Snake River basin. Introgression between Redband Trout and hatchery strains of coastal Rainbow Trout (<i>Oncorhynchus mykiss irideus</i>) was found in nearly half of the populations assessed, where high levels of admixture corresponded to increased heterozygosity. Independent of hybridization, the level of genetic diversity was found to be positively related to habitat extent, with populations occupying over 10&#xa0;km of stream exhibiting higher heterozygosity than those in under 5&#xa0;km of stream. While high levels of genetic diversity in nonhybridized populations may correspond to elevated adaptive potential, increased genetic diversity due to introgression represents a potential concern to fitness due to the effects of outbreeding depression.</p>