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Rhododendron brachycarpum is an ecologically important tree species with a narrow, fragmented geographic range in East Asia. R. brachycarpum is distributed primarily in Korea and Japan, with two small isolated populations in the Russian Far East. We obtained 124 samples from seven populations of R. brachycarpum, representing all geographical regions of its entire natural range, and we utilized microsatellite markers to estimate the level of genetic variation within and between populations. A total of 200 alleles based on 14 nuclear microsatellites loci were identified. High diversity (He = 0.556–0.626) was observed in populations from Korea and Japan. In contrast, in peripheral populations from Russia diversity was quite low (He = 0.100–0.369) with a high coefficient of inbreeding (FIS = 0.471–0.526). Strong population differentiation (FST = 0.356) and clear distinction among the geographical groups (FCT = 0.227) were revealed. Bayesian clustering and principal coordinate analyses indicated that two Russian populations, Sikhote-Alin and Iturup Island, represent extremes of two different migration routes, with one derived from the mainland and one from Japan. [ABSTRACT FROM AUTHOR]