A new species of deep-water dogfish shark, Squalus shiraii sp. nov., is described herein as endemic to the tropical waters off Southern Japan. This species has been largely misidentified with S. mitsukurii. However, morphological, meristic and morphometric evidence support it to be a separate and undescribed species. Squalus shiraii sp. nov. differs from this species by having body brown in colour dorsally, caudal fin with ventral and dorsal tips markedly tapered and broadly white, dermal denticles uniscuspidate and lanceolate and larger number of precaudal (91–94) and total vertebrae (120–123) (vs. body dark grey to black; caudal fin with ventral and dorsal tips rounded and not white in colour; denticles tricuspidate and rhomboid; 86–90 precaudal and 116–117 total vertebrae). Squalus shiraii sp. nov. is also clearly separated from other Japanese congeners which are herein revisited to include six species, based on the examination of over 150 specimens caught from Japanese waters that were available in ichthyological collections: S. mitsukurii, S. japonicus, S. acutirostris, S. brevirostris and S. suckleyi. Squalus mitsukurii, S. japonicus and S. brevirostris are re-described in detail and the neotype of S. japonicus is herein designated. Squalus acutirostris is treated as a valid species with occurrences in Japan, China and Taiwan and, thus, a provisional diagnosis is given, as well as an updated diagnosis of S. suckleyi. A key to Squalus species from the North-western Pacific Ocean is given and main morphological differences between S. shiraii sp. nov. and the closest related species are discussed.