The troglophilic spider subspecies Nesticus latiscapus kosodensis Yaginuma, 1972 is compared with its nominal species N. latiscapus Yaginuma, 1972 using an integrated taxonomic approach. Both morphological and molecular analysis suggest the two taxa are distinct, rejecting the status of subspecies. In the light of these results, N. kosodensis stat. nov. is elevated to species level and both species are redescribed. We expect that future revisions of Japanese Nesticidae will find that many currently designated subspecies are in fact distinct species. Taxonomic revision of long-established and unrevised subspecies may help to improve the conservation efforts aiming to protect the Japanese endemic cave fauna.