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Conservation genetic studies for Philippine pigs are essential to sustain global biodiversity. To study the phylogenetic relationship of Philippine pigs, 79 samples were collected from Ifugao (n = 41) and Kalinga (n = 38) provinces located in the Cordillera Administrative Region, northern Philippines. Mitochondrial DNA control region analysis was undertaken to investigate the phylogenetic relationship between the pig populations from the two provinces and other Asian and European pig breeds. Fourteen (14) haplotypes (H1–H14) were detected in the Ifugao and Kalinga samples. Several haplotypes – specifically, H1, H4, H9, H12, and H14 – formed an independent clade with the Type I Lanyu haplotypes, which are known to be unique in Taiwan pigs. The remaining haplotypes (H2, H3, H5–H8, H10, H11, and H13) clustered with the haplotypes of other Asian pig breeds within the major Asian clade. These results suggest the close relationship between Kalinga and Ifugao pigs and Type I Lanyu pigs. The existence of duplicate motifs also revealed that the native pigs from Ifugao and Kalinga belong to a distinct genetic lineage that clustered with other Philippine pig samples and separate from other Asian pigs, whereas the other samples may represent a recent introgression of modern lineages.

By analyzing the mitochondrial DNA (mtDNA) displacement loop (D-loop) region, we aimed to assess the genetic diversity of Philippine native pigs from Batanes, Quezon, and Marinduque and to determine the phylogenetic relationship between these subpopulations and other Asian and European pig breeds. Ear tissue samples were collected from the native pigs in Batanes (n = 17), Quezon (n = 37), and Marinduque (n = 40). Genomic DNA was extracted, and the D-loop sequences were amplified by PCR. The D-loop sequences of 94 Philippine samples were initially analyzed using the Kimura 2-parameter model and neighbor-joining method in MEGA7, identifying a total of 17 haplotypes designated as H1–H17. Notably, only eight haplotypes were specific to individuals coming from a particular province, whereas the remaining haplotypes were detected in samples from different provinces. Additional qualitative trait analysis that the majority of Philippine native pigs had black coat color, a plain coat pattern, short cylindrical snouts, straight head profiles, erect and forward-oriented ears, curly tails, and straight backlines. Phylogenetic analysis of the Philippine samples and 16 exotic pig breeds revealed that Philippine native pigs with H1 and H2 haplotypes formed a distinct clade with Taiwanese Type I Lanyu pig, whereas those with H3–H17 haplotypes clustered with other Asian and European pigs. Therefore, our findings suggest a close and unique relationship between Taiwanese Type I Lanyu and Philippine native pigs. The presence of several haplotypes also implies high genetic variation among Philippine native pigs. Specifically, the native pigs from Quezon and Marinduque are the most closely related, whereas those from Quezon and Batanes are the least closely related.