Phoebe chekiangensis is a rare and endangered species in China， and investigating its genetic diversity and genetic structure of populations provides a scientific basis for the effective protection and utilization. In this study， 15 pairs of SSR markers were used to analyze 175 germplasm resources from 10 populations by capillary electrophoresis. A total of 114 alleles （Na） were detected， with an average of 2.371 effective alleles （Ne） per primer pair. The polymorphic information content （PIC） of the SSR primers ranged from 0.323 to 0.844， averaging 0.629. The populations exhibited a moderate degree of genetic diversity （Ho=0.621， He=0.478）. The inbreeding coefficient within subpopulations （Fis） was -0.237， while the inbreeding coefficient for total population （Fit） was 0.082， indicating a high rate of heterozygosity. There was substantial genetic differentiation （Fst=0.275） and limited gene flow （Nm=0.763） among populations. Analysis of molecular variance （AMOVA） showed that inter-individual differences within populations accounted for 78.7% of the total variation （P<0.001）. Population structure and cluster analysis divided the 10 populations from different provenances into three groups， with some evidence of gene introgression between populations. Habitat fragmentation and human disturbance are likely the primary reasons of endangerment for P. chekiangensis. To protect its genetic diversity of P. chekiangensis， measures by combining in situ conservation and ex situ conservation should be implemented.