JC virus (JCV) genotyping is a novel method of tracing human migrations. In the present study, we used this method to gain insights into human expansions to the western Pacific. Using the whole genome approach, four genotypes of JCV (8A, 8B, 2E, and 7A) were previously detected in the island populations of the western Pacific. Using the same approach, we detected five genotypes (B1-a, B3-a, B3-b, SC-f, and SC-x) in Filipino populations (B3-b and SC-f corresponded to 2E and 7A, respectively). From these findings, it was concluded that seven genotypes of JCV were spread in the island populations in Southeast Asia and the western Pacific (these genotypes were tentatively designated as the ocean genotypes). Three of them (B1-a, B3-a, and SC-f/7A) occurred in the Philippines but did not occur in the western Pacific; two (B3-b/2E and SC-x) occurred in the Philippines as well as in the western Pacific excluding Guam; and two (8A and 8B) occurred only in the western Pacific. These regional distribution patterns for the oceanic genotypes suggested various human migrations to the Pacific, some restricted to islands near the Asian Continent and some extended far to Remote Oceania. Furthermore, our findings were consistent with the view that the Austronesians originated in an area of Southeast Asia, including the Philippines.