A new species of the genus Phallangothelphusa Pretzmann, 1965 is described, increasing the number of species in the genus to three: P. dispar (Zimmer, 1912), P. magdalenensis Campos, 1998, and P. juansei, new species. The new species is distinguished from its congeners primarily by the morphology of the first male gonopod, specifically the different shape of the distal and proximal projections of the mesial process; lateral process with distal bulge covered with rows of conspicuous spinules, and subtriangular outline of the apex. Phallangothelphusa is endemic to Colombia and its distribution comprises the upper and middle Magdalena valley region, including adjacent slopes of the eastern and central Andes, at elevations ranging from 300 to 1500 m. An updated key for the identification of the species is presented.