Genetic variation of the endemic tree species Abies veitchii var. shikokiana（AVS）, which is distributed only around the top of three mountains in Shikoku, was evaluated together with plus trees of A. veitchii var. veitchii（AVV） in Honshu using six nuclear SSR markers. Genetic diversity statistics were the highest in AVV plus trees, and among the three AVS populations, the eastern Mt. Tsurugi population exhibited larger values than the two western populations（Mts. Ishizuchi and Sasagamine）. The latter two populations have the westernmost distribution of A. veitchii, and their lower genetic diversity is presumably a result of isolation and strong genetic drift. The overall FST value（0.095） was relatively high, indicating genetic differentiation among populations. Principal coordinate analysis showed that the Mt. Tsurugi population has a more similar genetic composition to AVV plus trees, possibly related to its nearer geographic location to AVV. STRUCTURE analysis showed that the three populations of AVS belong to different main clusters, indicating that the original genetic variation occurred in different genetic backgrounds. The results obtained from the present study provide fundamental information to the ongoing programs for genetic management of AVS.