Although the ovary position is considered a stable character in angiosperms, Melastomataceae species have perigynous flowers in which the ovary varies from superior to inferior. Thus, we investigated the ontogenetic process involved in variation of the ovary position in Melastomataceae. We focused on histogenesis of the floral apex in search of developmental patterns for each type of ovary position. Six species in which the ovary varies from superior to inferior were chosen: Henriettea saldanhae, Leandra melastomoides, Miconia dodecandra, Microlicia euphorbioides, Rhynchanthera grandiflora, and Tibouchina clinopodifolia. Buds and flowers were processed for surface and histological examinations. The floral apex changes from convex to concave, resulting in a perigynous hypanthium. Cell divisions in the margins of the floral apex form an annular intercalary meristem that elevates the base of the primordia of almost all whorls. The joint growth of the carpel base with the gynoecial hypanthium originates semi-inferior ovaries in Leandra melastomoides, Miconia dodecandra, and Tibouchina clinopodifolia and inferior ovaries in Henriettea saldanhae. In Microlicia euphorbioides and Rhynchanthera grandiflora, the carpels are not affected by this hypanthial growth; flowers have a superior ovary. Changes in ovary position of Melastomataceae are due to intercalary meristematic activity, which is one of the main mechanisms for the origin of morphological innovations among plants. Our data illustrate the importance of the intercalary meristems in floral development, and we discuss the implications of this ontogenetic model for understanding the evolution of ovary position in Melastomataceae.