The Morros Garapenses Environmental Protection Area (EPA) is home to significant biodiversity and an important paleobotanical site, with Permian fossil records, being a strategic area for studies in Maranhão. The objective of this study was to provide a list of species of phanerogams from the Morros Garapenses EPA. The material was collected through the walking method on pre-existing trails at different elevations and phytophysiognomies. The collection, herborization, identification, and classification of species followed the usual methodology for this type of research. A total of 297 species distributed in 196 genera and 70 families were cataloged. The families with highest specific richness were Fabaceae (60 species), Malvaceae (20 spp.), Rubiaceae (18 spp.), Cyperaceae (16 spp.), Euphorbiacae (14 spp.), and Bignoniaceae (13 spp.). Forty-nine species were endemic to Brazil, fifteen are being reported for the first time from Maranhão, and five from Cerrado. Several phytophysiognomies were found in the area, namely, Cerradão (33 species), Campo sujo (7 spp.), typical Cerrado (154 spp.), veredas (10 spp.), riparian forest (5 spp.), and anthropized areas (5 spp.). The study revealed a significant number of species in the Morros Garapenses EPA, stressing the urgent need to create a management plan for the sustainable use of natural resources and recovery of degraded areas.