Taxus chinensis (Pilg.) Rehd is considered as one of the endangered species and only distributed in Northern Vietnam. The authors investigated the genetic variability and pattern structure of six populations sampled in five province of Northern Vietnam: Cao Bang; Ha Giang; Lao Cai; Hoa Binh and Son La. A total of leaves or inner barks collected from 148 individuals of six populations were used to assess genetic diversity using SSR. Six primer pairs were used in this study at population and species levels. Among six primers pair then 5/6 primer pair revealed polymorphic with PIC value (Polymorphic Information Content) varied from 0 (pt 30204) to 0.626 (pt15169), an average of 0.456. The study results showed an average number of allelesfor a locus was 1.142 (1.054 - 1.166), the average polymorphism 34.62 percent (25.00 percent - 41.67 percent). Observed heterozygosity averaged 0.107 (0.083 - 1.24) and expected one averaged 0.121 (0.101 - 0.138). The results suggest that small population sizes isolation have led to an increase of inbred individuals within populations. A number of measures applied to the conservation and sustainable development were also discussed.