The Philippine native pig (PhNP) is a unique genetic resource composed of multiple domesticated lineages and interspecific hybrids. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed seven PhNP populations ( = 20-27 samples each; Benguet [B], Kalinga [K], Nueva Vizcaya [N], Isabela [I], Quezon [Q], Marinduque [M], and Samar [S]) and four transboundary breeds present in the Philippines ( = 9-11 samples each; Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 20 microsatellite markers recommended by the ISAG-FAO. We tested for population structure at the island, region, and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by Bayesian clustering ( = 2) and Nei's genetic distance (100% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (: 0.737), a high allele count (: 7.771), and a low inbreeding coefficient (is: -0.040-0.125). Bayesian clustering supported genetic differentiation at the island ( = 2; North Luzon and South Luzon-Visayas cluster), region ( = 3), and population ( = 8) levels. The pairwise 'st between PhNP populations ranged from 0.084 (N and I) to 0.397 (Q and K), confirming that some PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that native pigs from B, K, I, Q, M, and S are unique genetic units for conservation. Furthermore, the small effective population sizes of B, I, Q, M, and S (: 3.9, 19.1, 14.2, 44.7, and 22.5, respectively) necessitate immediate conservation actions, such as incentivizing PhNP farming.