To estimate the genetic relationship of Vietnamese pigs in Central Highlands, we compared cytochrome b sequences of Vietnamese wild boars and Vietnamese domestic pigs with other Asian and European wild boars. The results showed that there were two wild boar populations locating in Vietnam Central Highlands including wild boars of group I and wild boars of group II. The Vietnamese wild boars of group II and domestic pigs were genetically close to Asian A1 and Asian A2 wild boar groups, whereas the Vietnamese wild boars of group I were genetically distinct from Asian A1, Asian A2 wild boar groups. The phylogenetic tree demonstrated that the Vietnamese wild boars of group I were clustered in one clade which was distinct from Asian wild boars and Europe wild boars. In addition, the Vietnamese wild boars of group I were estimated to have diverged from European wild boars at 421500 YBP, indicating that Vietnamese wild boar of group I could be isolated from other Asian wild boars. The single nucleotide polymorphism analysis showed that three Asian haplotypes were contributed in Vietnamese wild boars including A3 (TATG) haplotype in Vietnamese wild boar of group I and A1 (CATA) haplotype and A2 (CATG) haplotype in Vietnamese wild boars of group II. The A1 haplotype and A2 haplotype were also distributed in Vietnamese domestic pigs. Thus, there is a high possibility that Vietnam Central Highlands is a principal source for research on genetic diversity in Asian wild boar and domestic pig populations.