São Tomé and Príncipe's endemic species include several critically endangered and endangered birds found only on these islands: São Tomé fiscal (Lanius newtoni), São Tomé ibis (Bostrychia bocagei — considered possibly extinct), São Tomé grosbeak (Neospiza concolor), and Príncipe starling. The islands' forests, though heavily impacted by historic cocoa and coffee plantation development, retain important habitat for endemic species.
The ECOFAC (Central African Forest Ecosystems Conservation) program and BirdLife International partner Associação Birdlife São Tomé work on habitat protection and endemic species monitoring. Climate change represents an emerging threat to island endemic species through sea level rise and changed rainfall patterns.
Leatherback and green sea turtles nest on beaches on both islands, including remote beaches accessible only by boat. Príncipe's remote location has preserved some nesting beaches from human disturbance. Artisanal fishing bycatch represents the primary welfare threat to marine turtles. Conservation programs combine community engagement with beach protection.
The waters around São Tomé and Príncipe host diverse marine life including humpback whales (which calve in these waters), dolphins, whale sharks, and diverse reef fish. Humpback whales are observed year-round with peak activity July-September. The Portuguese firm Biopix conducts whale research from these waters.
São Tomé and Príncipe's agricultural economy historically centered on cocoa production. Smallholder farming of chickens, pigs, and goats for domestic consumption follows traditional practices. Animal welfare standards are not formally regulated, though the small community scale and subsistence nature of most animal keeping tends toward better individual attention than industrial systems.