Dipterocarpus alatus Roxb. ex G. Don is considered as one of the endangered species and cistributed in Southern Vietnam. The authors investigated the genetic pattern structure of two populations, one in Bu Gia Map National Park (Sinh Phuoc) and one Tan Phu Protective Forest (Dong Nai). A total of inner barks collected from 64 individuals of two populations, Bu Gia Map and Tan Phu were used to assess genetic diversity using 7 SSR primer pairs. PIC value (Polymorphic Information Content) varied from 0.130 (P214) to 0.335 (P120), an average of 0.253. The study results showed an average number of alleles for a locus was 1.174, the average polymorphism P = 78.57 percent (71.43-85.71 percent). Observed heterozygosity averaged 0.331 (0.286-0.335) and expected one averaged 0.306 (0.281-0.330). Shannon's index 1= 0.444 (0.42-0.467). The results suggest that although relative high level of genetic diversity, small population sizes will have to lead to an increase of inbred individuals within populations in future generations. A number of measures applied to the conservation and sustainable development were also discussed.