【Objective】The aims of this study were to investigate the effect of historic climate changes and habitat fragmentation on genetic diversity of Torreya grandis. 【Method】Ten populations were sampled over its entire natural range for genetic analysis using five chloroplast microsatellites loci. 【Result】A total of 28 haplotypes designed by 17 alleles at five polymorphic loci were detected across 300 individuals of the ten populations sampled. A single, common, and often frequent haplotype (H3 & H13) was detected in all extant populations of T. grandis. The genetic diversity (HE) of cpDNA detected within populations was 0.157 (0.098 to 0.211), lower than that in other eight conifer species previously reported. Based on paternally inherited markers, a lower level of genetic differentiation (0.020 3) was found in T. grandis than those previously reported for 37 other conifer species (0.165). Moreover, AMOVA analysis revealed that a significant amount of genetic diversity can be attributed to variation among populations (2.05%). 【Conclusions】In mountain regions such as Wuyi, Huangshan, Tianmushan and Kuaijishan mountains, possibly during the Last Glacial Maximum, a bottleneck may have been generated by repeated climatic oscillations and genetic drift may have played significant roles in shaping current haplotype distribution patterns.