Lithoxus jariensis is distinguished from its congeners L. surinamensis and L. pallidimaculatus by having an adipose fin (vs. adipose fin absent); from L. bovallii by the lack of an irregular concentration of chromatophores around the anal-fin origin and adjacent region (vs. present), and by having three dark bands in the caudal fin (vs. five dark bands); from L. lithoides and L. jantjae by having five branched rays in the anal fin (vs. four); from L. pallidimaculatus and L. raso by the lack of light spots on the body (vs. light spots on the body present); from L. jantjae by having 14 branched rays in the caudal fin (vs. 12); and from L. stocki by having medial premaxillary teeth with an enlarged and widened cusp (vs. cusps of all premaxillary teeth similar in size, not enlarged), and 5-8 dentary teeth (vs. 10-12). In addition, Lithoxus jariensis can be diagnosed from L. boujardi by having a greater adipose-spine length, 6.2-10.1% SL (vs. 3.6-4.7% SL), and by having a greater dorsal adipose-caudal distance, 12.0-16.5% SL (vs. 10.3-11.7% SL); from L. planquettei by smaller caudal peduncle depth, 7.6-8.7% SL (vs. 9.7-10.5% SL), and by having a straight adipose-fin spine (vs. a curved adipose-fin spine); and from L. stocki by having a shorter cleithral width, 27.8-31.2% SL (vs. 32.6-34.2% SL), and a greater dorsal-anal distance, 10.4-13.7% SL (vs. 8.8-10.4% SL) (Ref. 118148).