The purpose of this study was to identify the dimorphic structures of the orbita based on breed and sex factors through shape analysis across species. Additionally, the study aimed to ascertain the variability between the two species. A total of 86 (51 sheep—Akkaraman [Ak] and Morkaraman [Mk], 35 goats—Hair [Hr] and Honamlı [Hm]) skulls were used in the study. It was decided to designate 36 landmarks to represent the orbit's edge. In the principal component analysis, 68 PCs were calculated. It was determined that PC1, PC2 and PC3 explained the total variance in morphology by 26.909%, 16.147% and 13.616%, respectively. According to the cross‐validation results, the goats were grouped with 95% (Hm: 100%, Hr: 90%), while the sheep were grouped with 56% (Ak: 50%, Mk: 63%). Therefore, dimorphism among goat breeds on orbita shape was more pronounced compared to sheep. In the discriminant function analysis of the sex groups, Procrustes and Mahalanobis distance values in goats were 0.04425425 (p < 0.0001) and 5.3733 (p = 0.9550), in sheep 0.03513424 (p < 0.0001) and 7.1003 (p = 0.9414), respectively, was detected. According to the cross‐validation results, in terms of sex, goats were correctly grouped at a rate of 74% (F: 73%; M: 75%) and sheep breeds were correctly grouped at a rate of 72% (F: 77%; M: 66%). Factors such as habitat selection, breeding behaviours and ecological environment may show anatomical differences within breeds as well as between breeds. Therefore, various measurement techniques are used to reveal these differences. As a result, it is thought that the study will contribute to many disciplines, especially taxonomy and zooarchaeology, by analysing the shape of the orbita of sheep and goat breeds, the domestication of which dates back to ancient times, and revealing the similarities and differences between species and according to sex.