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The genetic structure of redband trout Oncorhynchus mykiss gairdnerii in the upper Snake River basin was investigated at various scales using 13 microsatellite loci. The majority of the genetic variation was partitioned between streams, although differentiation among watersheds was significant. This diversity was probably historically partitioned at the watershed scale when steelhead O. mykiss (anadromous rainbow trout) were present, with the exception of small, isolated, headwater streams where there may have been only resident trout. Genetic structure appears to have been altered by a combination of factors, including habitat fragmentation and hybridization with hatchery trout. Redband trout populations in the desert and montane environments both experienced reduced gene flow, but the desert populations displayed higher degrees of genetic differentiation. There was also a significant inverse relationship between the degree of genetic differentiation and the level of allelic diversity. Interspecific hybrids with cutthroat trout O. clarkii were detected within 9% of the sampled sites, but they made up only 2% of fish and were mostly confined to one sample location. In contrast, intraspecific hybrids with coastal rainbow trout O. m. irideus were detected within 31% of the samples sites and were more than twice as likely to be found where historical records indicated that stocking of hatchery rainbow trout occurred. The inclusion of intraspecific hybridized populations altered genetic structure by creating an artificial shared ancestry among populations from different drainages and led to higher levels of genetic variation in each of the populations. The threats of fragmentation and hybridization will need to be considered in developing conservation and management policies for redband trout in Idaho.