Mussel aquaculture is a significant industry in Eastern Canada where the blue mussel, Mytilus edulis and the bay mussel, M. trossulus co-occur. Generally mussel farmers associate M. trossulus with significant loss of productivity because of low meat yields and fragile shell. Previous studies on homogenous M. edulis populations have demonstrated that individuals showing the greatest performance are characterized by a lower standard metabolism related to higher multi-locus heterozygosity (MLH) level based on specific allozyme markers. These mussels rely less on their energy reserves to maintain vital functions and had more energy available to support physiological responses to stress at high temperatures. Mussels with high MLH levels also had lower mortality and higher growth rate. In this study, the metabolism performance of each species and their hybrids were estimated along with their respective MLH. For each species (M. edulis and M. trossulus) and hybrids, we observed that individuals with lower standard metabolic rate having higher MLH. Furthermore, M. edulis was characterized by higher MLH, lower standard metabolism and higher growth (estimated in length and mass) compared to M. trossulus and hybrids. We provide the economic and ecological implications of these findings for mussel aquaculture in Eastern Canada.