Hybridization between domestic pigs and wild boars of unknown origins has disrupted the precious gene pool of Vietnamese wild boar (Sus scrofa) populations in the Central Highlands. However, the genetic background of Vietnamese wild boars remains largely unknown. This study describes the complete mitochondrial genome of the Vietnamese Central Highland wild boar, a circular molecule comprising 16,581 base pairs (bp). The mitogenome contains 37 genes, which encode for 2 ribosomal RNAs, 22 transfer RNAs, and 13 mitochondrial proteins. It has a conserved gene order, gene orientation, and similar nucleotide composition indexes to other boars and pig breeds across the world. Notably, 232 nucleotide substitutions were detected when comparing this genome with 19 previously described Sus scrofa genomes. Partial cytochrome b gene analysis revealed the distribution of Asian haplotypes in the Vietnamese Central Highland Sus scrofa. A phylogenetic tree constructed from 32 Sus scrofa’s whole mitogenome sequences demonstrated the close relationship between Vietnamese wild boars and domestic pig breeds. The study provides additional insights into the genetics of Vietnamese wild boars, paving the way for future research in conservation, evolution, and breeding of Vietnamese wild boar populations.