The two laticaudine sea kraits, Laticauda laticaudata and L. semifasciata, are distributed in the tropical waters of the western Pacific and the northernmost limit of their breeding populations is considered to be the Northern Ryukyus, Japan. These two species, however, have been occasionally reported from the main islands of Japan, which are located further north. To determine the origins of such individuals, we examined partial sequences of the mitochondrial cytochrome b gene of one specimen of L. laticaudata from Yamaguchi and two specimens of L. semifasciata from Oita and Mie. Comparisons of the sequences with published data for apparently stable populations in the Ryukyu-Taiwan region revealed that sequence of the Yamaguchi specimen was identical with a haplotype previously detected from a broad range of the Ryukyu-Taiwan region and we could not specify its origin. Sequences of the Mie and Oita specimens were identical with, or very close to, haplotypes detected only from the Central Ryukyus and the Southern Ryukyus-Taiwan region, respectively. These results indicate that they were drifters from the Central Ryukyus and further south, corroborating the unconfirmed belief that sea kraits found on the main islands were accidentally transported by the Kuroshio Current from the south. Considering that both species exhibit certain degree of genetic differentiation among island groups in the Ryukyu-Taiwan region, the putative transportations by the Kuroshio seldom contribute to effective gene flow among local populations. The Kuroshio probably poses threats to their survival as the current may carry individuals out of their habitats and distributional range.