To examine the genetic origin of Ryukyu wild boar, we sequenced mitochondrial DNA (mtDNA: 574-bp) from Vietnamese wild boar and Vietnamese indigenous domestic pigs and compared these sequences with the mtDNA of Ryukyu wild boar by phylogenetic analysis. Numerous Vietnamese wild boars were genetically related to Ryukyu wild boar, suggesting that descendants of the ancestors of Ryukyu wild boar still inhabit Vietnam. The mtDNA sequences of Vietnamese indigenous domestic pigs are extremely diverse and are thought to have contributed to the diversity of mtDNA among East Asian domestic pigs.