Whip scorpions (Thelyphonida), comprising an order in the class Arachnida, are distributed from tropical to temperate zones. Two species occur exclusively in Japan and Taiwan, but the border of their distributional ranges is ambiguous in the Central Ryukyus (Japan). We collected new specimens from the Central Ryukyus and revealed that the border of distribution of the two species lies between the Central and Southern Ryukyus, i.e., the Kerama Gap. Moreover, the estimated divergence time (15.8 Mya) of the two species, based on the mitochondrial COI gene, was older than the recently estimated time (1.55 Mya) of formation of the Kerama Gap. These results highlight the risks of a priori assumption solely on the basis of geological data for applying it as a calibration point to some terrestrial animals in this region. Typopeltis stimpsonii was genetically divided into four lineages, two of which turned out to be endemic to the Okinawa Islands. All specimens from the main island of Japan and Shikoku were in one lineage, which was also found in the Amami Islands and Hachijojima Island. This suggests that these specimens may have been dispersed by human activity. Typopeltis crucifer included five genetic lineages. Species collected from Ishigakijima and Iriomotejima Islands were genetically diversified not between the borders of these islands but within Ishigakijima Island. This study also suggests that phylogenetic diversity of the species in the Southern Ryukyus have increased through two times of invasions from Taiwan.