The objective of this study is to assess genetic diversity within and between Dong Tao and Mong chicken linesas well as other Vietnamese chicken breeds using 20 Microsatellite markers. A total of 120 samples of 02 Dong Tao and 02 Mong chicken line collected (30 sample/line). The result indicated that genetic diversity of 02 Dong Tao chicken was at low level with the expected heterozygosuty from 0.54 to 0.55 whilegenetic diversity of 02 Mong chicken lines was at average level with the expected heterozygosuty of 0.60. Inbreeding coefficient of 4 chicken lines is very low. This 4 chicken lines represent the similar genetic structure and the genetic distance between them was low. The low genetic distance was found between 2 Dong Tao and 2 Mong chicken lines. The high genetic distance was found between these 4 chicken lines and Kien, Long XuandTai Đo chicken (Red Jungle Fowl). These 2 Dong Tao and 2 Mong chicken lines was divided into one group and differed from other breeds. Sub-structuring of the Vietnamese chicken breeds was related to their distant geographical distribution.