The present 3D Dataset contains the 3D models of two endocarps from the Oligocene of Baraval Quercy locality. These endocarps document new fossil genera within the Anacardiaceae family and illustrate the morphological diversity of this family during the Palaeogene. The CT-scan data were processed with ImageJ and Mimics Innovation Suite version 1.13 to reconstruct the specimens. Here we provide .stl files easy to read with the software Meshlab.