Polycentrus jundia can be distinguished from P. schomburgkii by the following characters: diagonal upper postorbital band being shorter than orbital diameter (vs. longer); median postorbital horizontal band present (vs. absent); subocular band being shorter than orbital diameter (vs. length of subocular band equal to or greater than orbital diameter; snout blunt (vs. protruding); mouth isognathous (vs. prognathous); serrations absent on lower edge of lacrimal or two tiny serrations at the posterior

end (vs. 8-14 conspicuous serrations distributed throughout the lower edge); posterior edge of vertical arm of preopercle fully serrated (vs. smooth edge); five pungent opercular spines, the three dorsalmost largest (vs. one or two short spines); subopercle widely serrated along most of the edge (vs. no serrations); cleithrum with serrations on posterior dorsal margin (vs. no serrations); interopercle with widely serrated edge (vs. clusters of three to five serrations along the edge of varying position between individuals); fourth pectoral-fin ray reaching vertical through anal-fin origin (vs. reaching vertical from spine III or IV of anal fin); 19-20 scales on dorsal-fin base (vs. 26-31); 12-14 scales on anal-fin base (vs. 16-20); 19-21 predorsal scales (vs. 28-30); and median opercular blotch absent (vs. present) (Ref. 102655).