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To better characterize the population dynamics of Vibrio parahaemolyticus (Vp) containing different virulence genes, two Vp strains were inoculated into seawater separately and incubated at temperatures (30 and 10 degree Celsius) mimicking summer and winter pre-harvest shellfish rearing seasons. The cellular responses of these two strains, one containing the thermostable direct hemolysin (tdh+) gene and the other one containing tdh-related hemolysin (trh+) gene, were studied at the transcriptomic level. Results showed that, at 30 degree Celsius, tdh+ and trh+ strains reached 6.77 +- 0.20 and 6.14 +- 0.07 Log CFU/ml respectively after 5 days. During this time, higher growth rate was observed in the tdh+ strain than the trh+ strain. When being kept at 10 degree Celsius, both Vp strains persisted at ca. 3.0 Log CFU/ml in seawater with no difference observed between them. Growth and persistence predictive models were then established based on the Baranyi equation. The goodness of fit scores ranged from 0.674 to 0.950. RNA sequencing results showed that downregulated central energy metabolism and weakened degradation of branched chain amino acid were observed only in trh+ strain not in tdh+ strain at 30 degree Celsius. This might be one reason for the lower growth rates of the trh+ strain at 30 degree Celsius. Histidine metabolism and biofilm formation pathways were significantly downregulated in both strains at 10 degree Celsius. No significant difference was observed for virulence-associated gene expression between 10 and 30 degree Celsius, regardless of the strains.