Ascertaining the genetic relationships between Austronesian populations is paramount to understanding their dispersal throughout the islands of the Pacific and Indian Oceans. The start of the Austronesian expansion has been dated to approximately 6,000 years ago, and from linguistic and archeological evidence, the origin of this dispersal may have been the island of Formosa. Consequently, the Taiwanese aboriginal populations and their phylogenetic relationship to the Austronesian-speaking groups from Madagascar at the occidental fringes of the expansion are of great interest. In this study, allelic frequencies from six polymorphic point mutation loci were assessed in the Austronesian-speaking populations of Madagascar, the Atayal aborigines of Formosa, and the general populations of Bali and Java. These allelic frequencies were compared and analyzed with the corresponding values from eight other worldwide populations from geographically targeted regions. The group from Madagascar is genetically distinct from their east-African neighbor from Zimbabwe. Our data also indicates that the Ami and the Atayal aborigines in the island of Taiwan, which occupy adjacent territories, differ sharply genetically. Genetic differences were also found between the populations of Bali and Java, belying their geographical proximity. Our results indicate that the east-African population from Madagascar phylogenetically segregates intermediate between mainland east-African and east-Asian groups, corroborating linguistic data indicating the Austronesian influence on this population.