Quaternary glacial cycles have drastically changed the Holarctic biota. Japan was mostly unglaciated and unoccupied by permafrost during the last Ice Age. Japan should have functioned as a glacial refugium for temperate freshwater invertebrates during several glacial cycles. Indeed, one of the oldest mitochondrial clades of Daphnia galeata was distributed only throughout Japan. Japanese populations of Daphnia dentifera also have much a higher genetic diversity and a stronger regional structure than populations in other distributional areas, indicating that Japan has provided mature habitats for the species. Consistently, recent phylogeographical studies have also indicated that Japan should be rich in regional population structures and endemic cryptic species of freshwater invertebrates. Previous phylogeographical study on Japanese D. dentifera and D. galeata revealed one endemic cryptic species lineage of Daphnia in Japan, which is closely related to D. dentifera and D. galeata. Here I found morphological difference in first antenna and head characteristic of adult male among the new species, D. dentifera, and D. galeata. The habitat of the new species restricted to alpine ponds, suggesting that Japan might also have functioned as an interglacial refugium for freshwater invertebrates.