The genetic population structure and demographic history of the whale shark Rhincodon typus, including 28 samples around Japan, the northernmost limit of distribution of the species, were examined based on partial sequences of the mitochondrial control region. Neighbor-joining tree and the minimum spanning network of haplotypes showed no clear phylogeographic structure. The pairwise Φ_ST values between each of the nine localities in the Indo-Pacific and the locality in the Atlantic were very high and significant, indicating the existence of genetic differentiation between the Indo-Pacific and the Atlantic. The existence of some level of genetic differentiation was also suggested between the Indian and the eastern Pacific, because the Φ_ST values were significant (though before Bonferroni correction) when comparing the Gulf of California in the eastern Pacific with three of the six localities in the Indian Ocean. In the Pacific Ocean, none of the Φ_ST values among the three localities (the Philippines and Taiwan, Japan, and Gulf of California) were significant, which indicates that migrations occur between the eastern and the western North Pacific as well as between north and south in the western North Pacific. The mismatch distributions and Bayesian skyline plots suggested that the Indo-Pacific and the Atlantic populations have different demographic history; population expansion had occurred in the Indo-Pacific while secondary contact among differentiated lineages was indicated in the Atlantic. Global distribution of effective population size (Ne) of the whale shark was estimated to be 63% in the Indo-Pacific and 37% in the Atlantic.