Tomiyamichthys alleni is described from eight specimens from Japan and Indonesia. The species is distinguishable from the only congener T. oni and closely related genus Flabelligobius in having the following combination of characters: occipital region narrow, equal to interorbital width, separated from upper margin of cheek by an irregularly curved groove; anterior oculoscapular canal with pores B′, C(S), D(S), F, and G′ (F located in groove between occipital region and cheek); first dorsal fin triangular, first and second spines elongated and filamentous; second dorsal and anal fin soft rays 10. The species occurs between 15 m and 40 m on fine sandy bottoms and is associated with the shrimp Alpheus randalli.