STRI has outstanding programs in forest and marine ecology, paleoecology, environmental monitoring, and conservation ecology. These programs include long-term environmental monitoring in Barro Colorado Island and at marine sites, studies of plant responses to elevated CO2 (carbon dioxide) levels and other stresses, a world-leading canopy biology initiative, and a large international network of forest-dynamics plots.

STRI's paleoecology program focuses on Miocene to Holocene changes in the Isthmus of Panama. Its conservation studies include the Biological Dynamics of Forest Fragments Project, a long-term study of forest fragmentation in the Brazilian Amazonia; a major reforestation initiative in Panama (PRORENA); and a dynamic program to identify novel pharmaceutical drugs from rainforest and marine organisms.