The Ezo brown frog (Rana pirica) and the Ezo salamander (Hynobius retardatus) are endemic species of Hokkaido, the northernmost island of Japan. Intestinal adult acanthocephalans are common in these amphibians. A molecular identification based on nuclear and mitochondrial DNA markers demonstrated that the parasites from the anuran and the urodelan are the same species. In the neighboring Honshu island, another acanthocephalan from ranid frogs (e.g. Rana japonica and Rana ornativentris) has been identified as Acanthocephalus lucidus. The counterpart species from the amphibians of Hokkaido was morphologically indistinguishable from A. lucidus. However, clear genetic distinctiveness between the two allopatric populations (separated by islands) indicated the entity of a cryptic species. A phylogenetic tree inferred from sequences of 28S ribosomal DNA showed that the acanthocephalans from Honshu and Hokkaido belong to the genus Pseudoacanthocephalus. Therefore, Pseudoacanthocephalus toshimai sp. nov. is proposed for the cryptic species in Hokkaido, together with the transfer of A. lucidus in Honshu to Pseudoacanthocephalus lucidus comb. nov. The present field survey further demonstrated Ligidium japonicum, an isopod crustacean living in the litter layer of forests, to be an intermediate host of the new species.