The genetic structure and relationships among four populations of the Philippine native cattle, namely: Ilocos, Batangas, Siquijor, and Philippine-Bali, were inferred from 16 DNA microsatellite loci by using F-statistics, for potential conservation purposes. Multilocus' FST values indicated that around 15.6% of the total genetic variation could be explained by differences between populations and the remaining 84.4% by differences among individuals. Interpopulation genetic diversity was evident in the phylogenetic tree constructed from the weighted Reynolds' distance (DR) matrix, and supported by results of correspondence analysis. Analysis of population admixture suggested that the individuals from these populations descended from three parental populations, presumably the zebu (Bos indicus), taurine (Bos taurus), and banteng (Bos banteng) cattle. This serves as a preliminary study to provide basic information for possible development of conservation programs for cattle in smallholder farms in the Philippines.