Abstract: Litsea szemaois is a critically endangered species endemic to southern Yunnan，China. We assessed the genetic variability within and among eight extant populations of this species using ISSR PCR (10 primers). We expected a low genetic diversity level, but our results revealed an extraordinarily high level of specific genetic diversity (at species level: percentage of polymorphic loci PPB=87.01%, effective number of alleles N_e=1.4006, Nei’s (1973) gene diversity H=0.2466, and Shannon’s Information index H_sp=0.3826; at population level: PPB=37.99%, N_e=1.2500, Nei’s (1973) gene diversity H=0.1418, and Shannon’s Informa-tion index H_pop=0.2088. The diferences among populations in levels of genetic diversity were very obvious, with the highest level (PPB=72.73%) in Mandian population and the lowest level (PPB=18.18%) in Jinghong population. A low level of genetic differentiation among populations was detected based on Nei’s genetic di-versity analysis (37%), Shannon’s diversity index (45%), and AMOVA (27.01%). This may result from out-breeding. Pairwise genetic identity (I) values among populations ranged from 0.8233 to 0.9761. There was no correlation between genetic and geographic distance among the populations studied. The influence of human activity and forest fragmentation may play a prominent role in creating this species’s current endan-gered status.