Phoebe chekiangensis is a rare and endangered species in China. The investigation on the genetic diversity and genetic structure of populations will provide scientific basis for the effective protection and utilization of germplasm resources of P. chekiangensis. Fifteen pairs of SSR markers were used to detect 175 germplasm resources from 10 populations by capillary electrophoresis to analyze the genetic diversity and genetic structure of P. chekiangensis. A total of 114 alleles (Na) were detected in 175 germplasms of P. chekiangensis by 15 pairs of primers, with an average of 2.371 effective alleles (Ne) per pair of primers. The polymorphic information content (PIC) of SSR primer ranged from 0.323 to 0.844, averaging at 0.629. The populations of P. chekiangensis showed a moderate degree of genetic diversity (Ho=0.621, He=0.478). The inbreeding coefficient within Subpopulations (Fis) was -0.237, and the inbreeding coefficient for Total populations(Fit) was 0.082, indicating that the heterozygosity rate was high. There was high genetic differentiation (Fst=0.275) and low gene flow (Nm=0.763) between populations. Analysis of molecular variance (AMOVA) showed that the inter-individual differences within the population were the main source of genetic variation, accounting for 78.7% of the total variation (P < 0.001). The population structure analysis and cluster analysis divided 10 populations of P. chekiangensis from different provenances into three groups, and there were some gene introgressions between populations. Habitat fragmentation and human disturbance may be the main reasons for the endangerment of P. chekiangensis, and measures should be taken to protect the genetic diversity of P. chekiangensis by combining in situ conservation and ex situ conservation.