Hemibrycon sanjuanensis can be distinguished from H. boquiae, H. brevispini, H. cairoense, H. colombianus, H. mikrostiktos, H. metae, H. palomae, H. rafaelense and H. tridens by having a circular or oblong humeral spot located two scales posterior to the opercle (vs. 3-4 scales in H. palomae, H. rafaelense, H. brevispini and H. cairoense, and 0-1 scales in H. metae and H. boquiae). It further differs from H. colombianus in having a round or oblong humeral spot (vs. rectangular). It can be diagnosed from H. beni, H. dariensis, H. divisorensis, H. helleri, H. huambonicus, H. inambari, H. jabonero, H. jelskii, H. mikrostiktos, H. polyodon, H. quindos, H. raqueliae, H. santamartae, H. surinamensis, H. taeniurus, H. tridens and H. yacopiae by the presence of melanophores on the posterior margins of the scales all along the sides of body (vs. absence of melanophores from margins of scales along entire length of sides of body). It is further distinguished from all congeners mentioned above by having the following characters: a wide, concave pelvicbone (vs. narrow and straight); middle part of the dorsal margin of the orbitosphenoid bone flattened and not in contact with frontal (vs. dorsal margin straight and in contact with frontal); ventral tip of supracleithrum bifurcate (vs. not bifurcate); six teeth in the outer premaxillary row arranged in a straight line (vs. five or fewer teeth in outer premaxillary row and not arranged in straight line, except H. cairoense with two to six teeth in the outer premaxillary row) (Ref. 98056).

Description: Anal-fin rays iii-iv,24-30 (Ref. 98056).