- Yellow-shouldered blackbird (Agelaius xanthomus)
- Puerto Rican parrot (Amazona vittata)
- Green mango (Anthracothorax viridis)
- Puerto Rican nightjar (Caprimulgus noctitherus)
- Puerto Rican emerald (Chlorostilbon maugeaus)
- Puerto Rican lizard‑cuckoo (Coccyzus vieilloti)
- Puerto Rican pewee (Contopus portoricenis)
- Adelaide's warbler (Dendroica adelaidae)
- Elfin-woods warbler (Dendroica angelae)
- Puerto Rican oriole (Icterus portoricensis)
- Puerto Rican bullfinch (Loxigilla portoricensis)
- Puerto Rican screech owl (Megascops nudipes)
- Puerto Rican woodpecker (Melanerpes portoricensis)
- Puerto Rican flycatcher (Myiarchus antillarum)
- Puerto Rican tanager (Nesospingus speculiferus)
- Puerto Rican spindalis (Spindalis portoricensis)
- Puerto Rican tody (Todus mexicanus)
- Puerto Rican vireo (Vireo latimeri)
- Camponotus kaura-[page needed] was first described by Roy R. Snelling & Juan A. Torres
- Solenopsis torrei-[page needed] was first described by Juan A. Torres
- Puerto Rico shipworm (Teredo portoricensis)
- Puerto Rican racer (Alsophis portoricensis)
- Mona ameiva (Ameiva alboguttata)
- Desecheo ameiva (Ameiva desechensis)
- Puerto Rican ground lizard (Ameiva exsul)
- Blue-tailed ground lizard (Ameiva wetmorei)
- Baker's worm lizard (Amphisbaena bakeri)
- Puerto Rican worm lizard (Amphisbaena caeca)
- Schmidt's worm lizard (Amphisbaena schmiditi)
- Puerto Rican dryland worm lizard (Amphisbaena xera)
- Cook's anole (Anolis cooki)
- Mona anole (Anolis monensis)
- Puerto Rican twig anole (Anolis occultus)
- Ponce anole (Anolis poncensis)
- Culebra Island giant anole (Anolis roosevelti)
- Puerto Rican garden snake (Arrhyton exiguum)
- Puerto Rican crested toad (Bufo lemur)
- Dryland grass anole (Ctenonotus poncensis)
- Mona ground iguana (Cyclura cornuta stejnegeri)
- Puerto Rican galliwasp (Diploglossus pleei)
- Puerto Rican cave dwelling frog (Eleutherodactylus cooki)
- Common coquí (Eleutherodactylus coqui)
- Mottled coquí (Eleutherodactylus eneidae)
- Golden coquí (Eleutherodactylus jasperi)
- Mona coquí (Eleutherodactylus monensis)
- Puerto Rican boa (Epicrates inornatus)
- Monito gecko (Sphaerodactylus micropithecus)
- Mona dwarf gecko (Sphaerodactylus monensis)
- Roosevelt's dwarf gecko (Sphaerodactylus roosevelti)
- Mona blindsnake (Typhlops monensis)
- Puerto Rican wetland blind snake (Typhlops rostellatus)
This is a list of all spiders endemic to Puerto Rico, according to Platnick.
- Ixodidae (ticks)
- Greater Puerto Rican ground sloth (Acratocnus major)
- Lesser Puerto Rican ground sloth (Acratocnus odontrigonus)
- Mauge's parakeet (Aratinga chloroptera maugei)
- Puerto Rican caracara (Caracara latebrosus)
- Puerto Rican plate-tooth (Elasmodontomys obliquus)
- Greater Puerto Rican agouti (Heteropsomys antillensis)
- Lesser Puerto Rican agouti (Heteropsomys insulans)
- Puerto Rican long-nosed bat (Monophyllus frater)
- Puerto Rican nesophontes (Nesophontes edithae)
- Puerto Rican flower bat (Phyllonycteris major)
- Corozal rat (Puertoricomys corozalus)
- Puerto Rican parakeet (Psittacara maugei)
- Puerto Rican Woodcock (Scolopax anthonyi)
- Puerto Rican barn owl (Tyto cavatica)
- Puerto Rican gharial (Aktiogavialis puertoricensis)
- List of amphibians and reptiles of Puerto Rico
- List of endemic flora of Puerto Rico
- List of Puerto Rican birds
- San Juan Botanical Garden
- The Puerto Rican pewee is not an official species recognized by the AOU. The species is a proposed split from the Lesser Antillean pewee (Contopus latirostris) by Rafaelle, H., et al. (1998) in A Guide to the Birds of the West Indies, Princeton University Press, ISBN 0691087369.
- This species was formerly categorized as Otus nupides but was subsequently renamed.
- This species was formerly a subspecies of Spindalis zena. In 1997 it was elevated to species status: O. H. Garrido; K. C. Parkes; G. B. Reynard; A. Kirkconnell; R. Sutton (1997). "Taxonomy of the Stripe-Headed Tanager, Genus Spindalis (Aves:Thraupidae) of the West Indies". Wilson Bulletin. 109 (4): 561–594.
- This species is also known as the North American worm lizard.
- This species is also known as pygmy anole.
- "Anolis poncensis". Zipecodezoo.com. Archived from the original on 27 December 2014. Retrieved 4 January 2009.
- This species has several common names. These are ridge-headed toad, lowland Caribbean toad, Puerto Rican toad and Sapo Concho.
- This species was formerly categorized as Peltophryne lemur but was subsequently renamed[permanent dead link].
- "Ctenonotus Poncensis". Zipcodezoo.com. Archived from the original on 27 December 2014. Retrieved 4 January 2009.
- Platnick, N.I. (2006). world spider catalog, version 7.0. American Museum of Natural History
- The greater Puerto Rican ground sloth became extinct approximately 3000–4000 years ago.
- The lesser Puerto Rican ground sloth became extinct approximately 3000–4000 years ago.
- The Puerto Rican plate-tooth or Puerto Rican paca became extinct approximately in the early 16th century.
- The Puerto Rican nesophontes became extinct approximately in the early 16th century.
- "Crocodiles Swam Atlantic? | KCRG-TV9 | Cedar Rapids, Iowa News, Sports, and Weather | Local News". Kcrg.com. 23 March 2007. Archived from the original on 15 May 2013. Retrieved 31 March 2013.
- Sociedad Ornitológica Puertorriqueña (in Spanish)
- Bosque Seco de Guánica (in Spanish)
- Integrated Taxonomic Information System
- Extinct vertebrates of the U.S.A., U.S. territories and Canada since 1492
- Rivero, Juan A. (1998). Los anfibios y reptiles de Puerto Rico. San Juan, Puerto Rico: University of Puerto Rico Press. ISBN 0-8477-0243-X.