Tropical perennial plants cultivated outside their place of origin call for major germplasm characterization and prebreeding work. For cacao breeding, the selection process has to optimize the weight of cacao beans produced per tree by increasing the number of pods produced, the number of seeds per pod (NoSP), and the mean weight of seeds produced (SW). NoSP and SW were studied over nine consecutive years in a collection of more than 200 clones. The number of ovules per ovary (NoOV) was also examined in a subsample of this collection in order to evaluate the ability to predict NoSP. NoSP and SW showed a relatively normal distribution with heritabilities of 0.29 and 0.51, respectively. The composite trait "mean seed weight per pod" showed a generalized extreme value distribution of intermediate heritability (0.43). NoSP and SW were found to be genetically independent. NoOV was highly heritable (h2=0.810), but it did not provide good prediction of NoSP. The largest seeds were observed in genotypes derived from crosses between cultivated cacao trees, which had been formerly domesticated. Domestication therefore favored seed size, while for the other traits examined, similar variation was found between wild and domesticated populations.