Beilschmiedia mannii (Meisn.) Robyns and Wilczek is an underutilised fruit tree valued for its nutritional benefits, but threatened by habitat destruction in Nigeria. Morphological characterisation was performed in order to elucidate the insufficient information on its morphological attributes in southwestern Nigeria. The study aimed at characterising the species population using the fruits, seeds, leaves, and the trees morphological attributes according to the habitats georeferenced by GPS. Different mother trees of the species were sampled for the study. Two distinct fruit colours (green and black) were identified, along with corresponding seed colours (red and cream). The species exhibited three primary fruit shapes, with corresponding seed shapes (ellipsoid, globose, and oval). B. mannii was encountered in the riparian, mangrove, and upland habitats. Significant differences were observed in the fruit weight, width, and length, seed weight, length and width, as well as mesocarp weight, leaf length and width between the two distinct colours, and amongst the shapes, and the habitats. The dendrogram-based clustering analysis revealed that the green morphotype and ellipsoid-shaped fruits formed the first cluster, while combinations of black and green fruits resulted in morphotypes with globose and ovate shapes in the second cluster. These findings highlight the presence of intraspecific diversity in the species with significant potential for species selection, breeding and improvement. This empirical data has important implications for the initiation of species domestication and conservation efforts.