The long observed disparity in fruit production among individual trees of the iconic African baobab, Adansonia digitata L. presents a potential challenge for the supply of fruit and seeds for food, medicinal and cosmetic purposes. Moreover, this disparity presents an unsolved mystery with ecological as well as economic implications. African baobabs are hermaphrodites where flowers have both male and female reproductive organs within the same flower. Here we evaluate the reproductive features, pollen-pistil interactions, and pollinator-attractant traits from South African baobabs to investigate whether trees with different fruit production levels have different floral features. We show that morphological traits highlight functional sex differences that match with average fruit production data of our sampled trees. Trees that produce more fruit comprised more functionally female flowers, whereas more functionally male flowers were characteristic of trees that did not produce many fruits. This difference may signify a shift in sex allocation in African baobabs, which suggests that baobabs might be functionally, or cryptically, dioecious. Collectively our data suggest that maintaining both tree types within a landscape is paramount for long-term sustainable harvesting of baobab fruit and seeds.