Eight-barbel loaches belonging to the genus Lefua have diverged into seven species in freshwaters of East Asia. Recent studies have discovered a new population in the Kuzuryu River drainage system of Fukui Prefecture, central Japan. Based on the results of the genetic analyses and morphological comparisons, we describe this population as a new species, Lefua nishimuraisp. nov. Body width, interorbital width, orbit diameter, preanal length, snout length, and the newly examined head width greatly contributed to the discrimination between L. torrentis, L. tokaiensis and L. nishimuraisp. nov. The new species can be distinguished from other congeners by combining the following characteristics: 1) eyes positioned dorsally on the head; 2) a narrow conspicuous longitudinal mark between the base of the outer rostral barbel and the eye; 3) small dark spots on the body, dorsal, and caudal fins; 4) a small dorsal fin and eye diameter; and 5) black spots above and below the base of the caudal fin. Based on the phylogenetic relationships of the genus, L. nishimuraisp. nov. is estimated to have diverged early from its common ancestor in central Japan. Understanding the natural history of this new species and implementing conservation measures are crucial because of its narrow, fragmented distribution and presence in vulnerable habitats.