To provide biological foundation for the utilization and breeding of Sinensis germplasm, ISSR and RAPD were applied to detect genetic diversity of 23 accessions of Sinensis germplasm. 79 bands were applied with 13 ISSR primers, of which 57（63.29%）were polymorphic, 57 bands were applied with 10 RAPD primers, of which 33（57.89%）were polymorphic. Effective number of alleles Ne, Nei’S index H, the Shannon information index were 1.4306 and 1.3601, 0.2305 and 0.2215, 0.3405 and 0.3145. The two molecular markers demonstrate that both ISSR and RAPD are efficient approaches for genetic diversity analysis of Sinensis germplasm and ISSR is more suitable comparatively in terms of reproducibility and ability of detecting genetic polymorphism. The influence of human activity and forest fragmentation may play a main role in creating this species’s current endangered status.