A new fish species of Hemibrycon is described from the San Rafael River, upper Cauca River, Colombia. H. rafaelense canbe distinguished from other species of the genus by the number of cusps on the teeth in the internal premaxilla row (3-5 vs. 5-7 except H. surinamensis), by the number of predorsal scales (10-12 vs. 12-17, except H. jelskii and H. orcesi), and by poscleithrum 1 (much closer to postcleithrum 2 vs. postcleithrum 1 and 2 clearly separated). Ecological data of the aquatic habitat of the new taxon are presented and keys to help identify known Colombian species are included.