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An inventory was prepared of ferns and lycophytes at Cuniã Ecological Station, South-Western Amazonia, Brazil, between 2010 and 2015, and 54 species were recorded. Lycophytes were represented by the families Selaginellaceae (two species) and Lycopodiaceae (one species), genera Selaginella and Phlegmariurus. Fifteen families of ferns were found, with most representatives from Hymenophyllaceae (11 species), Pteridaceae (nine species) and Polypodiaceae (seven species). Twenty five genera were identified; the most species rich were Trichomanes (seven species), Adiantum (six species), Asplenium, Lindsaea and Microgramma (four species each). Seven species or subspecies are new records for the state of Rondônia: Elaphoglossum obovatum, Lindsaea lancea var. remota, Oleandra articulata, Cochlidium linearifolium, Microgramma reptans, Adiantum tuomistoanum and Meniscium arborescens. Concerning life habit, 27 terrestrial species were recorded, 23 epiphytic species and four vines. Two terrestrial species were tree ferns. Fifty two percent of the species preferred one type of habitat, 12 species were exclusively found in riparian areas, 10 in terra-firme and six along the trails. The remaining 26 species (48%) were observed in more than one type of habitat. [ABSTRACT FROM AUTHOR]