The Kern River Rainbow Trout (Oncorhynchus mykiss gilberti) is a subspecies of rainbow trout endemic to the Kern River in central California. Previously found in the mainstem and tributaries of the Kern River, KRRT has been subjected to repeated introductions of both non-native rainbow trout and other native rainbow subspecies into its range. It is now listed in California as a “species of special concern.” Despite a historically distinct morphology and some preliminary genetic work verifying KRRT as a distinct group, introgression with introduced strains has been rampant, and many individuals no longer represent the original endemic form. It is currently unknown how many, if any, “pure” populations of KRRT are extant. My work will be to use single nucleotide polymorphisms (SNPs) to identify non-introgressed populations. I will use a targeted SNP isolation protocol to locate diagnostic SNPs, and genotype all putative KRRT populations. Those found to be distinct from introduced strains could then be used as hatchery broodstock and eventual restoration of the lineage within its native range.