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Variation at 14 microsatellite loci was surveyed in 26 chum salmon Oncorhynchus keta populations from Japan, one population from West Kamchatka and three populations from North America to determine population structure. Microsatellites were then applied to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index ( F st ) over all populations and loci was 0.031, with individual locus values ranging from 0.010 to 0.081. Seven regional populations were observed in Japanese chum salmon, with late-run populations from the Pacific Coast of Honshu the most distinct. Japanese populations displayed greater genetic diversity than did those in North America. Transplantation history in some Japanese river populations influenced their present genetic characteristics. Analysis of simulated mixtures from fishery sampling suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. Stock compositions for a 2005 sample of maturing, migrating chum salmon off the north-west coast of Hokkaido near the border of the Sea of Japan and the Sea of Okhotsk indicated that this region may be a migration corridor for Hokkaido populations from the Sea of Japan coast. Microsatellites have the ability to provide fine-scale resolution of stock composition in Japanese coastal fisheries.