Stephania is a genus of flowering plants in the Menispennaceae family, native to Southeast Asia and Australia. In the world, the genus includes over 40 species. In Vietnam, Stephania comprises 13 species with 4 species were listed in "Vietnam red data book". To study the relationships among Stephania species which were collected at Cuc Phuong National Park and its position in the genus, molecular phylogenetic trees have been constructed using Maximum parsimony method based on nuclear ITS region and the two chloroplast DNA regions, tmL intron and matK. the results indicated that there are two main clades in the genus. In which, SJ. group belongs to Stephania longa with 99 percent bootstrap support, and SR. group is in a close relationship with Stephania brachyandra with 94 percent bootstrap support. Additionally, the molecular phylogenetic analyses which conducted on the two chloroplast DNA regions, tmL intron and matK showed the level of change and branch off more clearly than the one using its nuclear ITS region.