Glyptostrobus pemilis (Staun) K.Koch is considered as one of the critically endangered conifer species and only distributed in Dak Lak province. the authors investigated the genetic variability and pattern structure of two populations sampled in two districts Eah Leo and Krong Nang, Dak Lak province. A total of leaves or inner barks collected trom 134 individuals of two populations were used to assess genetic diversity using chloroplast simple sequence repeat (cpSSR). Six primer pairs were used in this study at population and species levels. The study results showed Glyptostrobus pemilis had a low level of genetic diversity: an average number of alleles for a locus was 1.13 (1.07 - 1.19), the average polymorphism was 33.33 percent, observed heterozygosity was 0.076 in average (0.059 - 0.087) and expected heterozygosity ranged tron 0.056 to 0.019, with an average of 0.087. At Ea Rai (Eah Leo) population have high levels of inbreeding coeffient (Fis 0.2). These findings confirm high levels of genetic homozygosities at Ea Rai population and consequence of increase matings between very close relatives in small populations. Low genetic differentiation among the populations, indicating the high gene flow. The difference in genetic studies of 134 samples on the tree diagram by a factor of Jaccard's genetic similarity with UPGMA (Unweighted Pair Group Method) grouping type was divided into 13 main groups. Human activities which reduces population size and these consequences also affect to age structure in each population. A number of measures applied to the conservation and sustainable development were also discussed.