The eel goby, genus Taenioides (Gobiidae: Amblyopinae), inhabits muddy bottoms of estuaries or shallow areas of seas in the Indo-Pacific Ocean. Among congeners, T. cirratus (Blyth, 1860) has been thought to be distributed in Japan, but taxonomic confusions remain as to which scientific names are applicable to Japanese Taenioides species, or more fundamentally, how many Taenioides species are distributed in Japan, due in part to the rarity of this group in museum collections and the morphological similarity among species. To clarify the species diversity of the genus Taenioides in Japan, we conducted phylogenetic analysis on the basis of partial mitochondrial DNA sequences and morphological observation of more than 100 specimens. As a result, four distinct species were distinguished from each other, on the basis of both genetic divergences (2.9–5.7%, 16S rRNA gene) and morphological differences (i.e., degree of development of dermal folds on the head, numbers of barbels and vertebrae). Although the identifications of four species need additional verifications, they were identified as T. anguillaris, T. snyderi, T. gracilis and T. cf. kentalleni, and the species name T. cirratus does not seem to be appropriate to any of four detected species. Museum collections indicate that the two species, which are distributed in the main islands of Japan, were collected frequently and treated as a single species. The other two were each collected only from a single locality of Okinawa Island in this study, of which one seems to be uncommon worldwide as well.