The effect of two commercial in vivo transport methods (cardboard boxes and ixtle sacks) on the physiological condition of Japanese oyster (Crassostrea gigas) was evaluated. Total carbohydrates, glycogen, adenosine 5′-triphosphate (ATP) and related products, adenylate energy charge (AEC), and pH of transported oysters in simulated conditions were determined. The results showed that the ATP initial concentration was low from the beginning of the experiment, and AEC decreased in both transport methods. With respect to the total carbohydrates and glycogen, the samples maintained in cardboard box and ixtle sack decreased during transport, respectively. Similarly, significant changes in pH were observed for both methods. Our results showed that physiologically the best in vivo transporting method for Japanese oyster is in cardboard boxes.