Abstract Background In Aristolochia (Aristolochiaceae) flowers, the congenital fusion of the anthers and the commissural, stigmatic lobes forms a gynostemium. Although the molecular bases associated to the apical–basal gynoecium patterning have been described in eudicots, comparative expression studies of the style and stigma regulatory genes have never been performed in early divergent angiosperms possessing a gynostemium. Results In this study, we assess the expression of five genes typically involved in gynoecium development in Aristolochia fimbriata . We found that all five genes ( AfimCRC , AfimSPT , AfimNGA , AfimHEC1 and AfimHEC3 ) are expressed in the ovary, the placenta, the ovules and the transmitting tract. In addition, only AfimHEC3 , AfimNGA and AfimSPT are temporarily expressed during the initiation of the stigma, while none of the genes studied is maintained during the elaboration of the stigmatic surfaces in the gynostemium. Conclusions Expression patterns suggest that CRC , HEC , NGA and SPT homologs establish ovary and style identity in Aristolochia fimbriata. Only NGA , HEC3 and SPT genes may play a role in the early differentiation of the stigmatic lobes, but none of the genes studied seems to control late stigma differentiation in the gynostemium. The data gathered so far raises the possibility that such transient expression early on provides sufficient signal for late stigma differentiation or that unidentified late identity genes are controlling stigma development in the gynostemium. Our data does not rule out the possibility that stigmas could correspond to staminal filaments with convergent pollen-receptive surfaces.