Rhinogobius ogasawaraensis is distinguished from all congeneric species by the following unique combination of features: second dorsal fin rays I, 8-9, pectoral fin rays 18-20, predorsal scales 7-16, vertebral count 26, cheek with some red spots, nape with several longitudinal dark stripes, upper part of pectoral fin base with a dark blotch, intermittent dark dotted rows along middle axis of body, no saddle shaped patch of dark dots on dorsal side of body, ventral side of body yellowish white, caudal fin with some dark dotted rows on middle region and the base with a pair of dark brown bars which vertically to each other (Ref. 88999).