Hemibrycon sanjuanensis, new species, is described from the upper San Juan River drainage, Pacific versant, Colombia. It is distinguished from H. boquiae, H. brevispini, H. cairoense, H. colombianus, H. mikrostiktos, H. metae, H. palomae, H. rafaelense and H. tridens by the presence of a circular or oblong humeral spot that is 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 differs 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 in having melanophores on the posterior margins of the scales along the sides of body (vs. lacking melanophores on margins of scales along entire length of the sides of body). The new species differs from all congeners mentioned above in having, among other features, six teeth in the outer premaxillary row arranged in a straight line (vs. five or fewer teeth not arranged in straight line except H. cairoense with two to six teeth in the outer premaxillary row).