We used microsatellite and mitochondrial DNA-restriction fragment length polymorphism (mtDNA-RFLP) analyses to test the hypothesis that chum salmon Oncorhynchus keta and coho salmon O. kisutch in the Yukon River, Alaska, exhibit population structure at differing spatial scales. If the hypothesis is true, then the risk of losing genetic diversity because of habitat degradation from a gold mine near a Yukon River tributary could differ between the two species. For each species, collections were made from two tributaries in both the Innoko and Tanana rivers, which are tributaries to the lower and middle Yukon River. The results revealed a large difference in the degree and spatial distribution of population structure between the two species. For chum salmon, the microsatellite loci (F-statistic [FST] = 0.021) and mtDNA (F ST = -0.008) revealed a low degree of interpopulation genetic diversity on a relatively large geographic scale. This large-scale population structure should minimize, although not eliminate, the risk of genetic diversity loss due to localized habitat degradation. For coho salmon, the microsatellites (FST = 0.091) and mtDNA (FST = 0.586) revealed a high degree of interpopulation genetic diversity on a relatively small geographic scale. This small-scale population structure suggests that coho salmon are at a relatively high risk of losing genetic diversity due to lo-calized habitat degradation. Our study underscores the importance of a multispecies approach for evaluating the potential impact of land-use activities on the genetic diversity of Pacific salmon.