Astyanax courensis belongs to the A. scabripinnis species complex and is distinguished from other species of this complex by the number of scale rows between lateral line and pelvic fin origin (3-4 vs. 5-6), except from A. brachypterygium, A. burgerai Zanata & Camelier, A. goyanensis, A. intermedius Eigenmann, A. jenynsii, A. microschemos, A. rivularis Lütken, A. totae, and A. varzeae. It differs from A. brachypterygium, A. goyanensis, and A. totae by head length (24.9-28.2% SL, mean = 26.6 vs. 27.8-33.2, mean = 29.9, 27.7-32.3, mean = 31.6, and 27.9-32.8, mean = 29.7, respectively), and by the number of humeral spots (1 vs. 2, except in A. totae, which has one). It differs from A. burgerai and A. intermedius by shape of the dentary teeth (abruptly decreasing in size after fourth tooth vs. teeth gradually decreasing in size posteriorly), and orbital diameter (24.9-31.9% HL, mean = 27.9 vs. 34.6-40.6, mean = 38.0, 32.5-47.8, mean = 39.0, respectively); from A. jenynsii by the number of branched anal-fin rays (15-17, mean = 15.8 vs. 13-15, mean =14) and upper jaw length (40.6-50.0% HL, mean = 44.9 vs. 35.9-39.5, mean = 37.4); from A. rivularis by body depth (27.4-33.1% SL, mean = 30.5 vs. 35.0-46.0, mean = 40.3), and by the number of humeral spots (1 vs. 2); from A. varzeae by the number of lateral line scales (35-36, mean = 35.4 vs. 37-42, mean = 39), caudal-peduncle length (13.6-16.9% SL, mean =15.2 vs. 10.5-13.9, mean = 12.4) and orbital diameter (24.9-31.9% HL, mean = 27.9 vs. 30.9-44.5, mean = 37.9). Furthermore, it differs from A. microschemos and A. totae by the number of maxillary teeth (1 vs. 2-3 and 2-5, respectively). Astyanax courensis differs from only sympatric Astyanax species, A. goyanensis, by the number of pelvic-fin rays (8 vs. 7), and number of maxillary teeth (1 vs. 2-5), and by prepectoral distance (23.7-27.8% SL, mean = 26.4 vs. 27.7-32.0, mean = 30.4) (Ref. 84461).