Isla Margarita and particularly Cerro El Copey are especially important with respect to the numbers of endemic species they harbor. The island was connected to mainland until the Pleistocene. As a result, there is a predominance of typical continental bird families like Tinamidae, Dendrocolaptidae, Formicaridae and Furnaridae (Bisbal 2001), which are for example totally absent from the Antilles. 31 mammal species are found on the island, four of which (the red-tailed squirrel Sciurus granatensis nesaeus, the eastern cottontail rabbit Sylvilagus floridanus margaritae, the white-tailed dear Odocoileus virginianus margaritae, and the capuchin monkey Cebus apella margaritae) are endemic subspecies, with the main populations located inside the national park. The Margarita capuchin monkey is considered to be the country's most threatened primate species and is critically endangered (Rodríguez and Rojas-Suárez 1999).
The park has 67 reported bird subspecies (Rojas-Suárez et al. 1998) four of which are endemic to the island: the ferruginous pygmy owl Glaucidium brasilianum margaritae, the pale-breasted spinetail Synallaxis albescens nesiotes, Margarita's brown-throated parakeet Aratinga pertinax margaritensis and the yellow oriole Icterus nigrogularis helioeides. Two bird subspecies are endemic to the Eastern mountain range: the copper-rumped hummingbird Amazilia tobaci aliciae and the buff-throated woodcreeper Xiphorhynchus guttatus margaritae. The red-legged tinamou (Crypturellus erythropus margaritae) is a critically endangered bird species that is endemic to the park (Rodríguez and Rojas-Suárez 1999). Cerro El Copey has some of the only remaining habitat in the entire island for the scaled antpitta (anteater) Grallaria guatemalensis, a widely distributed species in the country. Another species that is restricted to the Venezuelan Caribbean and found in Cerro El Copey is the Margarita's carib grackle Quiscalus lugubris insularis (Bisbal 2001).
Very little is known on Margarita's reptiles and amphibians (Bisbal 2001); however, two endemic snakes (Drymarchon corais margaritae, Leptotyphlops albifrons margaritae) have been reported on the island (INPARQUES 2001).
A total of 14 mosquito species unregistered in Nueva Esparta State were collected during sampling at Cerro El Copey National Park. One of these 14 species had never been observed in Venezuela (Navarro 1998). A more thorough investigation of the park's invertebrate community is urgently needed.
Cerro El Copey's flora follows elevation gradients and follows a very similar pattern to the one observed in the Coastal Mountain Range (Huber 1999). Low to mid-sized semi-deciduous forests 10 to 25 m in height are found between 200 and 600 meters above sea level . The arboreal strata is relatively dense and you can find species like the naked Indian or gumbo limbo Bursera simaruba, Tabebuia billbergii, Croton multicostatus, Aspidosperma vargasii, Maytenus karstenii, Coccoloba coronata, Machaerium roboniifolium, Ximena americana, Neea anisophylla and the copey (Clusia major). This altitudinal range is home to two endemic species (Mikania johnstoni and Argythammia erubescen). Slash-and burn farming and other agricultural activities have had a major impact on the forest cover and plant composition (Hoyos 1985, INPARQUES 2001, World Wildlife Fund 2001).
The next altitudinal range (between 500 and 800 m) is covered by submontane evergreen forest with the canopy at an average height of 10-20 m. This is the home to such tree species as Tabebuia chrysantha, Myrcianthes compressa, Margaritaria nobilis, Guapira ofersiana, Nectandra coriacea, Dendropanax arboreus, Inga macrantha, Eutherpe karsteniana, Bactris setulosa, Chrysobalanus icaco and the endemic epiphytes Croton margaritensis and Clerodendrum margaritense (Hoyos 1985, INPARQUES 2001, World Wildlife Fund 2001).
The montane evergreen shrubs, also called dwarf humid forests, are dominant above 800 m (Hoyos 1985). These forests are composed of shrubby-herbaceous vegetation up to 3 m high; major species are Clusia flava, Blakea monticola, Clidemia hirta, Macleania nitida, Rapanea guayanensis, and the terrestrial and epiphytic forms of the bromeliad Glomeropitcairnia erectiflora (Hoyos 1985).
The vegetation at the top is dominated by ferns, herbazales, bromelias (Glomeropitcairnia erectiflora)
and forests of Clusia flava growing of form achaparrada due to the action of the winds.
A total of nine endemic species from this altitudinal range have been reported for the park: Bactris setulosa and Coccothrinax barbadense (Palmae), Blakea monticola (Melastomataceae), Inga micrantha (Leguminosae-Mimosaceae), Mikania johnstonii (Compositae), Epidendrum johnstonii (Orchidiaceae), Argythamia erubescens, Croton margaritensis (Euphorbiaceae) and Clerodendron margaritense (Verbenaceae) (Hoyos 1985). The bromeliad Glomeropitcairnia erectiflora is found only in Cerro El Copey, Paria and Trinidad. Some species such as Gettarda odorata, G. scabra, Cyathea arborea and Nectandra coriacea, are commonly found in the Antilles but have never been reported for continental Venezuela (Hoyos 1985).