Three Japanese fir species, Abies firma, A. homolepis and A. veitchii are distributed in cool temperature forests and their habitats are separated vertically. These species play an important role in maintenance of the forest ecosystem. In this study, genetic diversity and genetic structure of 42 populations from three species were analyzed using 21 nuclear simple sequence repeat (nSSR) markers. The sequence variation from five mitochondrial DNA (mtDNA) regions was also analyzed to infer population history of three Abies species. Because nuclear DNA and mtDNA have contrasted inheritance modes, they showed very different levels of gene flow. We detected higher genetic variation and lower genetic differentiation among populations in the biparentally inherited nSSR markers than in the maternally inherited mtDNA sequences. The nSSR markers revealed clear genetic differentiation among the three Abies species, and geographical cline of genetic diversity was found from northern to southern populations in A. firma. Also, the three Abies species shared the common mtDNA haplotypes and showed clear geographical cline in each species. These results suggest mtDNA capture through introgression among Abies species in each geographic region.