Asymmetry, the abnormality of an organism or a part of it from its perfect symmetry, is represented by three different categories: fluctuating asymmetry, directional asymmetry, and antisymmetry. Fluctuating asymmetry attributes to random developmental variation of a morphological character, whereas directional asymmetry attributes one of the body sides to be more prominent than the other. Antisymmetry appears whenever one body side of a biological body shows greater morphological appearance than the other. Since more environmental stress often produces greater effect of fluctuating asymmetry, it can be a good indicator of physiological stress in the morphological characteristic of a biological being. Applying, so far, the first geometric morphometric methods on any Byzantine fauna, this study aimed to determine the kind and direction of skull asymmetry occurred in Byzantine dog skulls. Aiming this, asymmetries in 16 adult Byzantine dog skulls unearthed form Yenikapi-Marmaray excavation (ancient Theodosius Harbor) in Istanbul, were compared with 39 adult skulls of modern pet dog breeds. Seventeen landmarks (3 midline and 14 bilateral) were selected on the digital pictures of the ventral aspect of each skull, and used for detailed analysis. The results showed a greater percentage of fluctuating asymmetry in the Byzantine dog skulls, suggesting them not to be the remains of pets or housed dogs but perhaps the labor or stray dogs in the Byzantine capital Constantinople.