Balancing the disparate objectives of fishery augmentation and conservation of an endemic population presents a substantial challenge. In the case of Warm Springs National Fish Hatchery (Warm Springs Hatchery), strategies for achieving both objectives included incorporation of natural fish into the hatchery broodstock and restricting proportions of hatchery fish on the spawning grounds. The hatchery has been more successful in implementing the latter, however, than the former. We analyzed seventy-six SNP markers in Spring Chinook Salmon O. tshawytscha collected from the Warm Springs River in 1976 – 1977 (prior to hatchery produciton) and 2001-2011 (post-hatchery) to examine whether the genetic characteristics of the endemic population had changed during that time. Pre- and post- hatchery collections clustered together when compared to Round Butte Hatchery (a nearby segregated program) and other Columbia River populations. The difference between pre- and post- hatchery collections was non-significant (AMOVA), but post hatchery samples exhibited significantly lower He. We observed some evidence of reduced effective size (Ne) and increased genetic drift in fish produced at Warm Springs Hatchery (relative to natural-origin fish), and even stronger evidence in fish produced at Round Butte Hatchery. We conclude that natural-origin fish returning to the Warm Springs River form a distinct group within the Interior Columbia Basin Spring-run lineage and have changed very little over the past eight generations. We further speculate that differences between hatchery- and natural- origin fish at Warm Springs Hatchery are expected to increase if hatchery operations remain static (little integration of natural-origin fish and incorporation of Round Butte Hatchery fish in broodstock).