Background: Vietnam's Song Ma village dog is a breed of indigenous dog found along the Ma River in Vietnam. They have many excellent traits, like their intelligence, agility, friendliness toward humans, and more importantly, they are very easy to train, and have the instinctive hunting capabilities of their wild canine ancestors. However, the exploration of genetic diversity and the origins of Song Ma village dogs in Vietnam have a serious lack of information. It is very difficult to promote the conservation of these dogs. Therefore, urgently needed in order to uncover and better understand the genetic architecture of Song Ma village dogs. Methods: We used 100 blood samples collected in Vietnam to estimate genetic diversity by sequencing the hypervariable-1 region. Results: We reported high levels of genetic diversity in the Song Ma village dog (Pi = 0.00912, Hd = 0.969, and Kt = 5.456). A total of 51 different haplotypes were identified in four haplogroups (A, B, C, and E). Furthermore, Song Ma village dogs were discovered in rare groups such as B1, B5, B6, B10, C2, and E1. Notably, no one in the haplogroup has the haplotypes (D and F). There were 49 single nucleotide polymorphisms, including 48 nucleotide base substitution or insertion changes and six nucleotide indel mutations found in the Song Ma village dog. A phylogenetic tree showed that Song Ma village dogs have a close relationship with dogs that originated from East Asia. Conclusions: This study has provided a valuable platform for breeding and conservation and management of the species in Vietnam.