Three new Selaginella species from Cuba, S. myriostachya, S. nanophylla and S. phiara, are described, illustrated with Scanning Electron Micrographs, and compared to similar species. Selaginella myriostachya and S. phiara are from Pinar del Río province, the latter one is also found in Isla de la Juventud special municipality, both in the western part of Cuba. In contrast, S. nanophylla is from Guantánamo, Holguín, and Santiago de Cuba provinces in the eastern part of the island. Information about their habitat, distribution, and conservation status is provided. Selaginella myriostachya lives in cave openings on limestone rocks in Mogotes formations; S. nanophylla is one of the smallest plants reported for the genus and seems adapted to serpentine soils. Selaginella phiara has idioblasts with several bright, papillae on the upper surface of median leaves and lower surface of lateral leaves, and short hairs on the upper surface of the apices of median leaves.