Background The purpose of this study was to explore whether domestication could lead to evolutionary changes towards flightlessness in the domestic duck (Anas platyrhynchos domesticus) compared to the cattle egret (Bubulcus ibis) as a nonflying and flying biological model, respectively. Bones of the pectoral girdle (scapula, clavicle, and coracoid) and the foramen triosseum were comparatively assessed using anatomical, radiographic, and 3D computed tomographic (CT) studies. Additionally, the muscles pectoralis and the supracoracoideus were histologically and immunohistochemically assessed. Results Among the differences observed, radiographically, the distance between the paired clavicles was significantly wider (p < 0.05) in the domestic duck (mean پ} SD 1.43 پ} 0.23 cm) compared with the cattle egret (0.96 پ} 0.13 cm). Unlike cattle egrets, there was no connection between the sternum and the hypocladium of furcula in domestic ducks. The scapula, clavicle, coracoid, sternum, and humerus were considerably longer in domestic ducks than in cattle egrets. The foramen triosseum appeared significantly (p < 0.01) wider in domestic ducks (0.7 پ} 1.17 cm) compared to cattle egrets (0.49 پ} 0.03 cm). Histologically, compared to cattle egrets, the muscle fibers in domestic ducks were loosely connected and contained fewer nuclei and perimysial/endomysial spaces. A higher myoglobin expression was evident in cattle egrets compared with domestic ducks.