Cardiogenesis is similar in all vertebrates, but differences in the valvuloseptal morphogenesis among non‐crocodilian reptiles, birds, and mammals are noted. The origin of mesenchymal structures such as valves that regulate the passage of blood and the formation of partial septa that prevent the complete mixing of oxygen‐rich and low‐oxygen blood present in adult chelonians are essential in the evolutionary understanding of complete septation, endothermy and malformations, even in mammals. In this context, this study analyzed the heart morphogenesis of Podocnemis unifilis (Testudines: Podocnemididae) from the 4th to the 60th day of incubation. We identified the tubular heart stage, folding of the cardiac tube and expansion of the atrial and ventricular compartments followed by atrial septation by the septum primum, ventricle septation by partial septa, outflow tract septation and the formation of bicuspid valves with cartilage differentiation at the base. The formation of the first atrial septum with the mesenchymal cap is noted during the development of the atrial septum, joining the atrioventricular cushion on the 17th day and completely dividing the atria. Small secondary perforations appeared in the mid‐cranial part, observed up to the 45th day. Partial ventricle septation into the pulmonary, venous, and arterial subcompartments takes place by trabeculae carneae thickening and grouping on the 15th day. The outflow tract forms the aorticopulmonary and interaortic septa on the 16th day and the bicuspid valves, on the 20th day. Therefore, after the first 20 days, the heart exhibits a general anatomical conformation similar to that of adult turtles.