Lannea species are among the fruit trees with high socio-economic importance in West Africa yet their intraspecific variability remains poorly studied, despite being essential for selection and domestication. This study aimed to characterize morphotypes based on 60 traits and 399 trees of Lannea acida A. Rich., Lannea microcarpa Engl. & K. Krause, and Lannea velutina A. Rich. in relation to environmental factors and local preferences in Burkina Faso. Ethnobotanical survey, direct observations and measurements were used to collect environmental, morphometric, categorical, phenological and organoleptic data for analysis. Findings revealed three morphotypes for each species and six ethnotypes for L. microcarpa. Morphotype 2 (early-fruiting, long inflorescence, acidic, medium fruit) and morphotype 3 (medium inflorescence, sweet, large fruit, large stem tip diameter) of L. acida are adapted to high temperatures. Morphotype 3 of L. velutina (yellow-fleshed, large fruits) is adapted to broad environmental conditions. Morphotype 1 of L. microcarpa (green-fleshed, acidic, small fruit, low endocarp) exhibits ecological adaptations to the Sudanian zone and is similar to ethnotype 2 (smaller, less juicy fruits, small leaves and thin bark), valued for its role in local diets. Morphotype 3 of L. microcarpa (yellow-fleshed, sweet, large fruit, large leaves, thick bark) is adapted to high temperatures and is similar to ethnotype 1 (large juicy fruits, broad leaves and thick bark) and ethnotype 3 (juicy, sweet fruits), preferred for its juicy and sweet fruits. Understanding the intraspecific diversity of Lannea species is essential for selecting the most suitable morphotypes for food production and domestication in agroforestry systems, particularly in arid and semi-arid environments, where resilience and adaptability are critical.