The Visayan warty pig (Sus cebifrons) is one of the world's most endangered pigs and is found only on the islands of Negros, Masbate and Panay in the Philippines. Its taxonomy and phylogeny has largely been based on morphology but a limited number of studies have been conducted to correlate morphological data with DNA sequences of key genes. In this study, PCR primers targeting mitochondrial 16s rRNA and cytochrome b genes were designed using DNAsis based on pig (Sus) mitochondrial DNA sequences available in the ENTREZ online database. The newly designed primers amplified mitochondrial 16s rRNA and cytochrome b genes using DNA templates from S. cebifrons, two other Philippine wild pig samples and two samples of the domesticated pig, Sus scrofia. The mitochondrial genes of the pigs used in this study were found to closely match their counterparts in the ENTREZ online database, with the mitochondrial 16s rRNA genes of wild pigs matching those of domestic pigs by as much as 98%, and the mitochondrial cytochrome b genes of wild pigs matching those of domestic pigs by as much as 95%. Sequence data and analysis of sequence alignments suggest that the S. cebifrons could be a distinct species and is phylogenetically separate from other species of wild pig from various localities around the world. Phylogenetic tree construction using data from the mitochondrial 16s rRNA and cytochrome b genes showed that S. cebifrons was grouped with mixtures of both European and Asian wild boar species in their specific clades but belonged to a separate clade, indicating a cross-continental introgression consistent with the introduction of Asian wild boars into European populations in the 19(th) century. The gene sequences in this study are the first ever reported for any wild pig species in the Philippines and the approach taken in phylogenetic analysis is expected to contribute to better conservation strategies for S. cebifrons.