A new cane-like begonia species, Begonia embera Jara & D.Franco, is described and illustrated. Morphological and molecular evidence suggest that it belongs to Begonia sect. Ruizopavonia. This species has been collected only in the Chocó Department, Colombia, growing by streams that flow into the Atrato river. We discuss its phylogenetic relationships, provide illustrations, and present the findings of an assessment of its conservation status.