To evaluate the evolution of lungs in archosaurs, it is essential to determine which traits are shared between crocodilians and birds and the role these traits play in the respiratory biology of these lineages. Both groups have unidirectionally ventilated lungs; however, unlike crocodilians which have mobile flexible lungs, the avian respiratory system is functionally and morphologically decoupled with an immobilized gas-exchanging lung, and flexible ventilatory air sacs. To investigate how these two divergent systems evolved, we used traditional and microCT, 3D digital modeling, and morphometry to examine the anatomy of the respiratory system across an ontogenetic series of eleven ostriches (Struthio camelus) and ten American alligators (Alligator mississippiensis). Left to right asymmetry and intraspecific variation was present in various regions of the bronchial tree in both taxa but was particularly evident in the medial (or cardiac) region of the alligator lung and the caudal aspect of the bronchial tree in both taxa. Five of fifteen lung metrics were significantly different between the two taxa, suggesting that these aspects of the lung are more plastic and should be explored in other species. In contrast to previous descriptions of the ostrich, our data demonstrate that regions of the axial skeleton are pneumatized by pulmonary diverticula that emerge directly from adjacent gas-exchanging tissues and not always the air sacs. Interspecific comparisons demonstrate multiple possible homologies between the bronchial trees and overall lung structure, suggesting that certain aspects of the bronchial tree may have been conserved across Archosauria.