Dioecy is a sexual system characterized by the complete separation of male and female floral functions between individuals of the same species. Some species of the Meliaceae family are considered functionally dioecious because of the lack of noticeable morphological differences between their male and female flowers. Here, we performed morphological and anatomical studies of the flower of Cabralea canjerana subsp. polytricha to identify sexual dimorphism between its male and female flowers. We also examined aspects of floral and pollination biology that may be related to the sexual system of this subspecies. The field studies were carried out in two Brazilian Cerrado reserves. Cabralea canjerana subsp. polytricha presents similar female and male flowers that open between late afternoon and early evening and are visited by moths in the evening and small bees during the daytime. Floral biology dynamics indicate that moths are the primary pollinators. The similarity between male and female flowers may facilitate flower recognition by the visitors, enhancing pollen flow between morphs. However, compared with female plants, male plants have longer inflorescences and more flowers with larger anthers, which may attract more pollinators and disperse a higher number of pollen grains to the stigma of female flowers. Male flower carpels have ovules smaller than the female flowers. Most female flowers presented ovules with structurally normal embryo sacs. Male flowers may occasionally have normal ovules and produce fruits, which indicates that dioecy may not be complete, probably due to the functional aspect of its sexual system.