Most species in the genus Selaginella (Selaginellaceae) are susceptible to desiccation, while a few species are able to withstand the extreme desiccation, recover metabolic functioning, and grow rapidly after rehydration. However, there is limited information about the anatomical features of the resurrection species in Selaginella. In the present study, we compared the microphyll micromorphology and ultrastructure of two resurrection species (S. pulvinata and S. sanguinolenta), and two non-resurrection species (S. kraussiana and S. chrysocaulos). Compared with the two non-resurrection species, the two resurrection species had most of their stomata distributed on the adaxial surface of microphylls that were tightly attached to stems, and possessed smaller and thicker microphylls, smaller stomatal size, higher stomatal density, thicker epidermal cell walls, more chloroplasts, and denser cytoplasm. These micromorphological and ultrastructural features of the two resurrection species were beneficial in reducing the transpiration and dehydration damage and could be considered as ecological adaptations to xeric environments.