In the present study, we used morphological and genetic analyzes to distinguish bones of domestic boars from those of wild boars. We analyzed 65 Sus bones (cranium, mandible and teeth) stored in three research institutes in Vietnam and in a village in Vietnam. Based on comparison of bucco‐lingual measurements of mandibular parts, the 58 specimens were morphologically classified into two size groups: a large bone group and a small bone group. Analysis of 572‐bp mitochondrial DNA (mtDNA) sequences indicated that the large bones had genetic links to wild boar lineage including Ryukyu, Taiwan and Korean wild boars, and that the small bone group was closely related to East Asian domestic pigs. The phylogenetic analysis and parsimonious networks constructed among mtDNA haplotypes belonging to Ryukyu wild boar lineage showed that the Ryukyu wild boar is closely related to the Vietnamese wild boars, and uniquely miniaturized on their islands after the Ryukyu archipelago became isolated from the Asian continent.