The subterranean amphipod genus Pseudocrangonyx is diverse in Far East Asia, including the Japanese Archipelago. However, Pseudocrangonyx species have not been recorded from the Ryukyu Islands, which extend southwest of the Japanese Archipelago. This study describes a new species of Pseudocrangonyx, Pseudocrangonyx dunan sp. nov., from Yonaguni Island, Ryukyu Islands, Japan. Phylogenetic analyses revealed that P. dunan sp. nov. is a sister species to Pseudocrangonyx sp. 4 from Honshu Island, Japan. In addition, three monophyletic groups were found in Pseudocrangonyx, although the phylogenetic positions of several species remain unknown. Our divergence dating indicates that the differentiation of major lineages of Pseudocrangonyx, which contains species from both the Asian continent and the Japanese Archipelago, is concentrated around 20 MYA. These results suggest that the opening of the Sea of Japan is one of the major factors promoting the speciation of Pseudocrangonyx endemic to the archipelago.