Respiration rates of various geographical strains of Crassostrea gigas were compared to assess the respiratory expenditure as a physiological indicator of catabolism (cost of maintenance). Parental oysters, sampled in France (Marennes-Oléron), Japan (Hiroshima), Taiwan (Tunkang) and Spain (Cadix), were differentiated by both their geographic origin and by mitochondrial DNA markers, allowing the distinction between the two closely related taxa Crassostrea gigas and Crassostrea angulata. After reproduction of these parental oysters, respiration rates of spat of each strain, reared under common controlled conditions, were individually estimated at 20 °C by using a volumetric microrespirometer. Our results demonstrated that physiological variability existed among the Crassostrea gigas strains and is likely to be related to physiological differences between geographical regions and/or genetic adaptations. The French strain showed the highest rates (0.71 μL·h−1), while the Japanese, Taiwanese and the hybrid between Spanish and French strains consumed less, 0.53, 0.43 and 0.40 μL·h−1, respectively. Our results confirmed the discrepancies previously suggested between Crassostrea gigas and Crassostrea angulata. Comprehensive physiological assessments should be carried out over a wide temperature range to confirm our results and to further evaluate growth potential. Appropriate decision making based on these studies will help future shellfish management in shellfish rearing areas such as the overstocked Marennes-Oléron Bay.