Conservation efforts aimed at Pacific salmon (Oncorhynchus spp.) populations have frequently utilized artificial propagation in an attempt to increase fish abundance. However, this approach carries the risk of unwanted changes in the genetic characteristics of the target population and perhaps others that might incidentally be affected. We used genetic monitoring techniques to estimate the amount of introgression that has occurred from nonnative hatchery stocks into native populations and to determine the extent of genetic changes that have occurred in association with supplementation efforts over the past 20–50 years in Snake River Chinook Salmon O. tshawytscha populations from northeastern Oregon. A total of 4,178 fish from 13 populations were genotyped for 12 microsatellite DNA loci. Expected heterozygosity values for each sample ranged from 0.707 to 0.868. Estimates of the effective number of breeders per year in the naturally spawning populations ranged from 20.6 to 459.1, whereas in the hatchery populations they ranged from 33.8 to 1,118.8. We found that introgression from the Rapid River Hatchery stock was particularly noticeable in the early 1990s but that it appears to have had a substantial effect on only two of the native populations (Lookingglass Creek and the upper Grande Ronde River) despite the ample opportunities for introgression to occur. All seven of the native populations sampled have maintained their levels of within‐population genetic diversity throughout the sampling period. Overall, this region's supplementation efforts appear to have had a minimal effect on the genetic diversity of its Chinook Salmon populations.Received October 9, 2012; accepted March 25, 2013

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