All the islands of the park, especially Coiba, are uniformly covered by dense forest vegetation, the latter being in more than 80% of its primary forest species like surface where "Mary" (Calophyllum spp), "secuara" (predominantly Tetragastris panamensis), "I tangaré" (Carapa guianensis). In the area of ​​the geological fault one of the most abundant species is the Podocarpus guatemalensis. 

There are also seven large mangrove areas covering an area of ​​1758 hectares, where the species of red mangrove (Rhizophora mangle) and m predominate. piñuelo (Pelliciera rhizophorae). Other major and minor vegetation are cativales comprising some 758 hectares, of Cativo (Prioria copaifera), the Acorns (Mora oleifera) and Sangrillalles (Pterocarpus officinalis). Fosteri Psychotria (Rubiaceae), Fleischmannia coibensis (Compositae) and Desmotes incomparabilis (Rutaceae) are new species endemic to Coiba.