Laboratory-produced juvenile individuals of the species Mytilus chilensis, M. galloprovincialis and their hybrids were subjected to physiological measurements under an experimental diet of Isochrysis galbana (30 × 106 cells L−1), 13°C temperature and a salinity of 30 psu. Pure species individuals showed a higher clearance rate (CR). Mytilus chilensis had a CR of 1.13 L h−1, while M. galloprovincialis registered only 0.78 L h−1. Also, pure taxa registered higher values (above 70%) of absorption efficiency when compared with hybrid individuals. Ammonia excretion in M. chilensis and M. galloprovincialis was 1.5% and 0.4%, respectively, while hybrids registered significantly lower values. Under these experimental conditions, M. chilensis registered the highest scope for growth (P < 0.05), compared with M. galloprovincialis and their hybrids. However, the net growth efficiency index (K 2) in hybridization type I (♀Mg × ♂Mc) was higher (P < 0.05) than other experimental groups. The invasive mytilid M. galloprovincialis showed values that are very similar to those obtained with the hybridization I group (♀Mg × ♂Mc). Finally, we discuss that water temperature is an important factor in the biogeographic separation of both species and the potential effects that the settlement of the invasive species may have for Chilean mussel production.