Aim: The aim of this study was to reveal the dimorphic structures of the foramen magnum and condyle occipitalis through an interspecies shape analysis and to determine the variability between sheep and goats.

Materials and Methods: The study includes data from 81 skulls (46 sheep and 35 goat) for this aim. The foramen magnum frame shape and the condyle occipitalis variation were determined using type I (anatomical) and type III (semilandmarks).

Results: Accordingly, was determined 30.76, 14.94 and 14.07 of the total shape variation of PC1, PC2 and PC3, respectively. It was determined that condylus occipitalis was primarily responsible for the shape variation according to PC1, and foramen magnum was responsible for the secondarly. It was found to explain the shape variation of the right condyle occipitalis to a great extent compared with PC2, while in PC3, it caused the entire right condyle occipitalis to explain the shape variation of the extreme lateral corner of the left condyle occipitalis and the left edge of the foramen magnum. The discriminant function analysis determined the Procrustes and Mahalanobis distances to be 0.12293879 (p < 0.0001) and 67.7482 (p < 0.0044), respectively.

Conclusion: As a result, the geometric morphometry method is regarded to be a useful tool for detecting changes in skull shape between species and can thus be used successfully for taxonomic, archaeological, and forensic research.