Sindora siamensis Teijsn. ex Miq. is a large evergreen tree and of Critically Endangered (CR) species in southern Vietnam. 60 individuals of 6 naturally distributed populations classified by habitat for this species were analyzed. Inter simple sequence repeat (ISSR) markers were employed to investigate the genetic variability in. Results showed higher at the species level (PPB=94.96%, HT=0.280; IT=0.417), but lowers at within populations, which Pop4 lowest genetic diversities (PPB=44.44%; Hs =0.173; Is =0.2422) and the highest value of Pop3 (PPB=73.92%; HeS=0.2247; Is =0.3546). The hierarchical analysis of molecular variant revealed differentiation among population (14%), which was confirmed by the gene differentiation coefficient (GST= 0.1871) and occurred gene flow. The GST value translated into corresponding low level of gene flow (Nm=2.1720). And it’s showed that the migration among the six populations was low, which is 2.03%.