Recent phylogenetic studies using mtDNA and allozymes have revealed the presence of large genetic differentiation within a Japanese clawed salamander, Onychodactylus japonicus, suggesting the presence of several cryptic taxa in this species. Based on morphological analyses, we describe one of them from the Tsukuba Mountains of Ibaraki Prefecture, in the Kanto district of eastern Honshu, as a new species, Onychodactylus tsukubaensis. It is a member of the japonicus species complex of Onychodactylus, and differs from the other species of the complex by a relatively short tail, wide head, and large number of vomerine teeth.