Plant sexual reproduction depends notably on the development of the gynoecium that contains the ovules. Early ovule development relies on differential growth of placental structures controlled by the concerted actions of hormones and key regulators. Among these regulators the CUP-SHAPED COTYLEDON genes play a crucial role in gynoecium patterning and ovule development. Indeed, CUC1 and CUC2 control the initiation of ovule primordia via an auxin-dependent mechanism. Here we highlight an additional role for CUC2 and CUC3 in ovule individualisation. While CUC1 and CUC2 are broadly expressed in the medial-tissue of the gynoecium, CUC3 is specifically expressed between ovule primordia at early stages. Consistent with this expression pattern, we show that the cuc2cuc3 double mutant specifically harbors defects in ovule separation, producing fused seeds sharing the seed coat. These results highlight a partially redundant role for CUC2 and CUC3 in ovule individualisation. Functional analyses in Cardamine hirsuta show that NAM/CUC3 transcription factors also control ovule development in this species. In situ hybridization expression studies in more phylogenetically distant species reveal a conserved NAM/ CUC3 expression pattern between ovule primordia. Taken together these results highlight an ancient role for NAM/CUC3 transcription factors in ovule separation and shed light on the conservation of regulatory mechanisms in the development of innovative structure.