Vibrio parahaemolyticus and Vibrio cholerae are ubiquitous to estuarine and marine environments. Thes two species found in Mediterranean coastal systems can induce infection in humans. Environmental isolates of V. cholerae (n = 109) and V. parahaemotycius (n = 89) sampled at different dates, stations and water salinities were investigated for virulence genes and by a mutilocus sequence-based analysis (MLSA). V. cholerae isolate were all ctxA negative and only one isolate of V. parahaemolyticus displayed trh2 gene. Most Sequence Types (ST) corresponded to uique ST isolated at one date or one station. Frequent recombination events were detected among different pathogenic species, V. parahaemotyticus, V. cholerae, Vibrio mimicus, and Vibrio metoecus. Recombination had a major impact on the diversification of lineages. The genetic diversity assessed by the number of ST/strain was higher in low salinity condition for V. parahaemolyticus and V. cholerae whereas the frequency of recombination events in V. cholerae was lower in low salinity condition. Mediterranean coastal lagoon systems housed V. cholerae and V. parahaemotyticus with genetic divesities equivalent to the worldwide diversity described so far. The presence of STs found in human infections as well as the frequency of recombination events in enviromental vibrios populations could predict a potential epidemiological risk.