We describe and illustrate Selaginella rachipterygia Valdespino, Cornejo & C. López as a new species found on the inter-Andean eastern slopes of the Central Cordillera of Colombia and on the slopes on both sides of the Andes of Ecuador and compare it to S. flagellata Spring. Selaginella rachipterygia is notable for its often flagelliform branch, stem, and strobilus tips, which are often gemmiferous, and by its lateral leaves perpendicular to the main stems below the first branches, which give the stems the appearance of having wings. In addition, we document the expanded distribution range of S. simplex Baker to include Panama and Ecuador. Finally, we contrast S. simplex with the similarly small-sized species S. correae Valdespino and S. minima Spring, which overlap either in part of or throughout their distribution ranges.