Astyanax joaovitori is distinguished from its congeners belonging to the A. scabripinnis species complex by the following combination of characters: lateral dark stripe beginning immediately behind the upper margin of the opercle; presence of a single vertical humeral dark blotch; a scattered pattern of dark chromatophores below lateral line, at the abdominal region; anal fin with 15 to 20 branched rays; 33 to 36 perforated scales on lateral line; dentary teeth decreasing abruptly in size from the fourth or fifth tooth onwards; and 13 or 14 scales around caudal peduncle (Ref. 116165).