Parodon atratoensis differs from all congeners in having just the first dorsal-fin ray unbranched (vs. two, except in P. magdalenensis); two dorsal longitudinal stripes that end at adipose-fin origin (vs. ending at upper caudal-fin lobe or absent). It is distinguished from P. magdalenensis by a series of transverse dorsal bands ending at adipose fin (vs. ending at upper caudal-fin lobe or absent); in having the axillary scale 2-3 normal scales in length (vs. usually one, rarely two scales in length; except in P. buckleyi). It also differs in the number of cusps on the premaxillary teeth (12-13 vs. 15-19 in P. carrikeri; 7-12 in P. bifasciatus; 9-12 in P. pongoensis). It can be differentiated from P. guyanensis by the number of teeth on the premaxilla (4 vs. 5) and from P. pongoensis and P. moreirai by the presence of a lateral band with projections above and below (vs. absence of projections in such band) and the number of scales in the lateral line (37-38 vs. 40-42 in P. moreirai). From P. suborbitalis it is distinguished by the number of cusps on premaxillary teeth (12-13 vs. 15-17); number of branched pectoral-fin rays (12-13 vs. 14-17); preanal scales (23-24 vs. 24-27); two light dorsal stripes uniting at adipose fin (vs. stripes ending at upper caudal-fin lobe) and transverse dorsal blotches ending at adipose fin (vs. dorsal blotches ending at base of upper caudal-fin lobe). From P. hilarii it differs by the absence of spots above lateral stripe (vs. present); the number of preanal scales (23-24 vs. 24-28). It differs from P. nasus by the presence of elongated projections of the lateral stripe (vs. rounded projections) and the number of cusps on premaxillary teeth (12-13 vs. 13-15).