Knowledge of oilseeds plants’ traits and features is fundamental to understanding the natural selection process and improving conservation programs through species selection. As a forest oilseed, Ricinodendron heudelotii is the object of growing interest among value chain actors, who are increasingly interested in its intrinsic characteristics. To date, there is a lack of information on plant morphological traits for the selection of the best genotype, especially as far as seed and kernel traits are concerned. The aim of this study was to make a typology and establish the relationship between seed and kernel traits of Ricinodendron heudelotii, depending on provenances represented by wild populations of trees in southern Benin. We sampled the provenances constituted equally and per tree, ten random samples each of fruits, seeds, kernels, and shells were collected for measurement. Hierarchical classification, common component analysis, Pearson’s, and Chi-square association tests were performed for statistical analysis. Substantial variation between seed and kernel traits was observed between and within provenances. High coefficients of variation for the quantitative descriptors (length, width, and mass) of seeds and kernels appear to be the essential traits that discriminate the plant into two morphotypes. Furthermore, seed and kernel characteristics show a significant positive correlation with these discrimination criteria. The upper morphotype contains accessions from three provenances with huge seeds and kernels but few seeds per fruit, while the lower morphotype includes the other provenances with tiny seeds and kernels. The results of the study provided essential information that could be an avenue for improvement with further biochemical and molecular characterization studies.