French Guiana is an overseas territory of France which harbours a tropical rainforest with a vast biodiversity, including ca. 1800 tree species. This forest suffers pressure from mining, climate change, and logging in the permanent forest domain. Conserving the rainforest and achieving sustainable timber production to meet the demands of a growing human population is a considerable challenge. We present an overview of our ongoing research in ecological and conservation genomics in several tree species of French Guiana. We showed how tree species complexes of the genera Symphonia and Eschweilera are adapted to microenvironmental conditions relating to moisture, soil chemistry, and light. In the most harvested timber tree Dicorynia guianensis we use estimates of regional and local population genetic structure, population demographic histories, and genomic signatures of adaptation to derive sustainable management guidelines under future climates. We have used a combination of microsatellites, genomic, and transcriptomic approaches to characterise the genetic diversity of the highly endangered Aniba rosaeodora, and identify genes implicated in the production of rosewood essential oil. We also present tools under development for simplified field delimitation of morphologically similar species of Eschweilera in view of sustainable harvesting of common species while conserving rare related species.