Strychnos spinosa Lam. is an important wild edible fruit tree (WEFT) that is increasingly threatened due to anthropogenic pressure. Despite its remarkable socio-economic potential, commercial plantations for the species are rare. Characterization of the genetic diversity and potential of WEFT is a prerequisite for domestication and genetic improvement. This study assessed the morphological diversity and differentiation among populations of S. spinosa across a climatic gradient (Sudano-Guinean vs Sudanian zones) in Benin, West Africa. Morphological data were collected on 81 trees and 810 fruits of S. spinosa from 7 populations in the two climatic zones using nine phenotypic descriptors. Descriptive statistics and multivariate analyses were used to describe and partition differences among trees and study populations. Results showed highly significant differences (P ≤ 0.001) among populations for all measured traits. The within-population variation accounted for the highest proportion (53–90%) of the total variation. Strong and positive correlations (r = 0.91–0.99; P < 0.05) were observed among trunk and fruit traits except for tree height and fruits’ seed weight suggesting that fruit traits (fruit mass, pulp mass, seed number, ratio) can be predicted from trunk traits (dbh). Cluster analysis distinguished three distinct groups of S. spinosa in Benin. Population from Bassila phytodistrict in the Sudano-Guinean zone showed superior phenotypic traits (e.g. tree diameter, fruit mass, and pulp mass) indicating a high potential for selection for domestication purposes. Our study revealed marked phenotypic diversity of S. spinosa in Benin and provides relevant information for domestication and harnessing of S. spinosa genetic resources.