ABSTRACT. The taxonomic status of Pinus henryi, a rare species endemic to China, is still ambiguous. In this study, the genetic relationships among P. henryi and its congeners (P. tabulaeformis, P. tabulaeformis var. mukdensis, and P. massoniana) were revealed using multiplexed microsatellite markers, including chloroplast microsatellites, nuclear microsatellites, and expressed sequence tag microsatellites. The results refute the hypothesis that P. henryi is a subspecies of P. tabulaeformis or P. massoniana and support the suggestion that it may be a distinct species closely related to P. tabulaeformis.