Manonichthys scintilla is distinguished from congeners by the following characters in combination: scales to preopercular angle 3–4; second segmented pelvic-fin ray longest; no dark eye stripe on head; no dark bar on posterior body; pelvic fin with red to orange coloration indistinct and confined to distal part of fin; and caudal fin rounded with posterior margin truncate (Ref. 88961).

Description: Characterized by purplish head grading to yellow on body; side of body with 10-11 narrow brown stripe; dorsal fin with pale spots; caudal and anal fins yellow basally; anterior lateral line scales 22-27; predorsal scales 17-19; depth of body 28-30 % of SL (Ref. 90102).