Genetic diversity of four Vietnamese indigenous chicken breeds including Lien Minh (GLM), Dong Tao (GDT), Nhan (GNH) and Chin Cua (G9C) were evaluated using mitochondrial DNA (mtDNA) D-loop sequence polymorphism. 1,050 bp of D-loop region of 66 individuals was amplified, sequenced, and analyzed. Comparative alignment results showed that the four local chickens shared 96.6% - 99.9% nucleotide identity with each other. Results of D-loop sequencing analysis revealed 53 variable sites (gaps included) in native Vietnamese chickens as compared to reference sequence (AB268540). Among them, there were six nucleotide deletions, ten nucleotide insertions (positions) and 37 nucleotide substitutions (sites). The estimated haplotype diversity (Hd) within breed was relatively high, ranged from 0.824 (GNH) to 0.913 (GLM). Phylogenetic study based on hypervariable region of 455 bp D-loop showed that all Vietnamese native chicken breeds were distributed over 16 haplotypes belonged to five haplogroups A, B, C, D and E, of which clade B was dominant. Individual of GLM, GDT, and G9C breeds clustered mainly in clade B (34/48) and GNH chicken (18 individuals) belonged to clade C and D. This study shows the relatively high genetic diversity of native Vietnamese chicken breeds and contributes to the conservation and breeding strategy of indigenous chicken in Vietnam.