A new species of Zanthoxylum L. (Rutaceae) from Colombia and Brazil is described here, based upon morphological characters. Zanthoxylum palustre Londoño-Ech. & Reynel is distributed in lacustrine, riverine, and swampy environments at very low altitude, and belongs to Zanthoxylum sect. Macqueria Comm. ex Triana & Planch., the largest section of the genus; it is distinguished by several vegetative and reproductive characteristics.