Glossogobius mahalonensis is distinsguished by the the following characters: absence of all head pores; mental fraenum indistinct and covered by sensory papillae; cheek naked; operculum with few embedded small scales dorsally; predorsal scaled to near eye; pectoral base scaled; prepelvic area partly scaled, naked anteriorly; second dorsal fin-rays usually I,9; anal-fin rays usually I,8; pectoral rays 14–16; predorsal scales 17–24; pelvic fin oval, length about twice width, rays not thickened; gill opening broad, reaching to a point below end of pupil to posterior end of eye; midsides with horizontally elongate small brown spots (smaller than pupil length) forming a broken horizontal line, often indistinct, not visible in dark specimens; first dorsal fin blue in life; cheek papilla lines with multiple rows of papillae, forming distinct lines (Ref. 99936).