The presence of Vibrio parahaemolyticus in bivalve mollusc is an important cause of foodborne illnesses, and their levels are influenced by environmental changes, such as temperature and salinity. Clams are common species in estuaries and are used in environmental monitoring programmes. Present study compared the uptake and retention of nonpathogenic V. parahaemolyticus by two species of clam (Ruditapes decussatus and R. philippinarum), cohabitating in a closed system. Results showed no significant differences were found between both species of clams. Bacterial levels are following a similar trend with values between 3.48 and 3.70 log CFU/g for R. decussatus and between 3.15 and 3.49 log CFU/g for R. philippinarum. So, in the absence of water renewal, high and stable levels of V. parahaemolyticus were observed in cultured clams after exposure. Changes in physical parameters should be taken into account to design surveillance programmes in bivalves, and sampling should focus on species that have faster filtration rates at that water temperature since they potentially represent the worst-case scenario.