The carabid beetle Nebria taketoi Habu, 1962 is endemic to the high-altitude mountains of Honshu, Japan; due to its rarity, it is one of the least taxonomically studied species among Japanese Nebria. This study taxonomically revised N. taketoi based on morphological comparisons, mainly of the endophallus in males, and geometric morphometrics of the pronotum, a taxonomically useful external character. Specimens previously identified as N. taketoi were found to belong to at least two species: N. taketoi, with a currently confirmed distribution in the northern Hida Mountains (type locality: Mikurigaike, Mount Tateyama), and N. kobushicola sp. nov. from the Okuchichibu and Yatsugatake mountains (type locality: Mount Kobushigatake). Species identities in populations from other localities could not be determined, as male specimens for endophallus examinations were unavailable. However, some populations may consist of species distinct from N. taketoi and N. kobushicola, based on their distribution and morphometric features. Based on comparative morphology of the endophallus, N. kobushicola shares features more similar to N. niohozana Bates, 1883 and N. dichotoma Sasakawa, 2020 than to N. taketoi.