Pentaclethra macrophylla Benth (Fabaceae) has emerged as one of the top underutilized agroforestry species with considerable economic and nutritional value in West and Central Africa where the species is endemic and exploited by farmers. However, the species suffers from a level of exploitation that is unsustainable. This dramatically decreases the natural resource base. Key information such as tree variation is needed to develop an efficient strategy for its domestication. This study therefore assesses the species phenotypic variation in two populations in the forest zone of Cameroon. Overall, 49 trees (19 in Lomie and 30 in Djoum) were sampled. Tree characteristics (diameter at breast height (DBH), height, crown diameter), pod (number of seeds per pod), seed (width, length, thickness, weight) and kernel traits (weight) were recorded. All these parameters were subjected to a combination of multivariate, PCA and cluster analyses. Results revealed four clusters of P. macrophylla trees with cluster IV considered as the best because it contains four elite trees (LOM/PM/09, LOM/PM/13, LOM/PM/15 and LOM/PM/16) with desirable tree characteristics. Clusters were further considered as different groups of trees, and seeds and kernel traits variation assessed using ANOVA analysis. Significant differences in mean kernel weight occured between groups. Cluster IV presented the highest mean kernel weight (19.25 ± 0.16 g), while cluster III had the lowest (13.28 ± 0.57 g). Within cluster IV, the highest kernel weight (25.83 ± 5.62 g) was found in tree number LOM/PM/09. Kernel weight was found to be positive and strongly correlated (r = 0.95) with seed weight. We can conclude that there is phenotypic variation between the trees of P. macrophylla in terms of DBH, height, crown diameter, number of seeds, seed width, seed length, seed thickness, seed and kernel weight. Results obtained in this study could serve as a useful guide for the selection of targeted P. macrophylla trees either for domestication or for conservation purposes.