We conducted a survey on the mycorrhizal status of neotropical ferns, focusing on previously neglected taxa. These include the filmy ferns (Hymenophyllaceae), grammitid ferns (Polypodiaceae), and the genus Elaphoglossum (Dryopteridaceae). Samples were collected at different sites in southern Ecuador, Prov. Loja, Morona-Santiago, and Zamora-Chinchipe. Among the 85 investigated species (101 samples, 10 families), 19 were associated with arbuscular mycorrhizal fungi (AMF) and 36 were infected by dark septate endophytes (DSE), which are identified as ascomycetes and here considered as a kind of mycorrhiza similar to the ericoid type. The roots of 30 species (including all non-grammitid Polypodiaceae and half of the Elaphoglossum species) were free of evident fungal infection. AMF were frequent in terrestrial species (29.10% of species, or 48.49% of infected terrestrial samples). DSE prevailed in epiphytic species (58.62% of species, or 96.15% of infected epiphytic samples) and were also common in terrestrial samples of predominantly epiphytic species.