We investigated phylogenetic positions of Cynops pyrrhogaster from nine localities in the central and southern parts of the Izu Peninsula using the mitochondrial cyt b gene. We revealed that the central and the southern populations are phylogenetically remote. The central Izu lineage belongs to the CENTRAL clade occurring from Chubu through Kinki to Chugoku districts, whereas the southern Izu populations form a lineage sister to the NORTHERN clade, which is distributed in Tohoku and Kanto districts. Genetic differentiation between the southern Izu lineage and the NORTHERN clade is relatively large with the uncorrected p-distance of 3.4%, which suggests their divergence at 3.31 MYA. This estimation indicates their genetic differentiation prior to 1.0 MYA, when the Izu Peninsula was formed through collision of a paleo-oceanic island with Honshu. These results indicate that the ancestor of the southern Izu lineage diverged from the NORTHERN clade somewhere in northern Honshu and then invaded the Izu Peninsula newly formed by collision and settled there. The central Izu lineage thereafter also invaded the peninsula, confining the range of the preceding southern Izu lineage to its current range.