There are nearly a thousand threatened species of vascular plants in the Philippines and of which about 12% are lycophytes and ferns. However, there are not enough data on the distribution of the species. Thus, the threatened lycophytes and ferns were determined based on field surveys in four protected areas in Mindanao, namely Mt. Apo Natural Park, Mt. Kitanglad Range Natural Park, Mt. Malindang Range Natural Park, and Mt. Hamiguitan Range Wildlife Sanctuary. The conservation status assessment was based on the Department of Environment and Natural Resources DAO 2017-11 updated list of threatened plants of the Philippines. A total of 45 species of threatened lycophytes and ferns was documented belonging to 16 families and 25 genera. Of these, three species are Critically Endangered, 23 Endangered, 15 Vulnerable, and three are other threatened species. Families with the highest number of threatened species are Cyatheaceae, Polypodiaceae, Lycopodiaceae, Ophioglossaceae, and Psilotaceae. The Critically Endangered species are Platycerium coronarium, Phlegmariurus magnusianus, and Helminthostachys zeylanica. The threatened species endemic to the Philippines are Phlegmariurus magnusianus, Alsophila apoensis, A. atropurpurea, A. hermannii, A. fuliginosa, A. heterochlamydea, A. negrosiana, A. rufopannosa, Lindsaea hamiguitanensis, Tmesipteris zamorarum, Aglaomorpha cornucopia, and A. sagitta. The highest number of threatened taxa was observed in the Mt. Apo Natural Park (29 species), followed by the Mt. Kitanglad Range Natural Park (28 species), Mt. Malindang Range Natural Park (27 species), with the lowest number in the Mt. Hamiguitan Range Wildlife Sanctuary (19 species). Most of the species were recorded in the lower and upper montane forests. The occurrence of threatened and endemic lycophytes and ferns in the four protected areas calls for a strict implementation of the ordinances necessary for a long term conservation and protection of the species.