Root endophyte colonization was investigated in 32 fern and lycophyte species of 11 families collected from the Celaque National Park in Honduras. Arbuscular mycorrhizae (AM) were found in 11 plant species (34%) of Anemiaceae, Gleicheniaceae, Ophioglossaceae, Pteridaceae, Selaginellaceae, Thelypteridaceae, and Woodsiaceae. The abundance of arbuscular mycorrhizal fungi (AMF) in roots varied with particular species, ranging from 4% (Sticherus underwoodianus) to 78% (Thelypteris patens). The morphological AM colonization pattern of all investigated species was of the Paris-type. The mycelium of dark septate endophytes (DSE) was found in 19 species (58%), and was observed both in the roots of plants that were colonized by AMF and were devoid of AM association. However, in both cases the percentage of root colonization by these fungi was low. Exceptions were Asplenium serra, Elaphoglossum erinaceum, Lellingeria prionodes, and Lycopodium thyoides, where abundant DSE hyphae were observed. Our results are the first detailed report of both AMF and DSE associations of these plant species. Moreover, the mycorrhizal status of 27 plant species is reported for the first time.