Floral diversity of Croton, the second largest genus in Euphorbiaceae, is currently under-explored. Several clades demonstrate an unusual floral morphology, e.g., lower or higher stamen number, bilateral symmetry and reduced ovary, but have never been investigated in a comparative study with typical Croton. This study examined morphology and ontogeny of flowers in nine Croton species from different clades within the genus with light and scanning microscopy, resin sectioning and micro-computed tomography. In staminate flowers, great variations of stamen number and arrangement are observed. The ancestral androecium likely consisted of two or more whorls with the outermost antepetalous stamen whorl developing centrifugally. Modification by reduction of the antepetalous whorl resulted in an outer alternipetalous stamen whorl in Croton section Moacroton, subgenus Quadrilobi. Several species in the subgenus Geiseleria show an independent reduction of stamen numbers by absence of a centrifugal development with the antepetalous whorl the first whorl to develop. Petal losses are observed in the distantly related C. setiger and C. dioicus. Chaotic stamen arrangement is found in C. celtidifolius (subgenus Adenophylli) as a result of a secondary stamen increase. In pistillate flowers, reduction of carpel numbers happened three times in the subgenus Geiseleria. C. monanthogynus has a bicarpellate ovary, while in C. setiger and C. michauxii the ovary is monocarpellate. Reduction of carpel number is linked with merism change and perianth reduction. The ovary in C. michauxii has basal placentation which is unique among all Croton. Moreover, strong bilateral sepals and nectaries are observed in species from section Julocroton. Therefore, the floral diversity of some species in the genus Croton could be explained by developmental modification of an ancestral form via reduction, rearrangement of stamen whorls, and symmetry shifts.