Multi-locus sequence types (MLST) from a global collection of Vibrio vulnificus isolates were analysed for the contribution of recombination to the evolution of two divergent clusters of strains and a human-pathogenic hybrid genotype, which caused a disease outbreak in Israel. Recombination contributes more substantially than mutation to generating strain diversity. For allelic diversity within loci, the ratio of recombination to mutation events is approximately 2:1. The role of recombination relative to mutation in the generation of new MLST variants of V. vulnificus within the clusters is comparable to that of other highly recombining bacteria such as Neisseria meningitidis. However, across the divide between the two major clusters of V. vulnificus strains, there is substantial linkage disequilibrium, lower estimates for recombination rates and shorter estimates of recombination tract length. We account for these differences between V. vulnificus and N. meningitidis by attributing them to the presence of the unusual genetic structure within V. vulnificus. The reason for the presence of distinct and divergent genomes remains unresolved. Two possible explanations put forward for future study are first, ecologically based population structure within V. vulnificus and second, a recombination donor from a phenotypically differentiated species.