Vibrio vulnificus is a leading cause of shellfish-associated food-borne illness. US regulations stipulate shellfish processing procedures to limit V. vulnificus densities; however, the effect of these procedures on V. vulnificus strain distribution and/or genetic diversity is unknown. Vibrio vulnificus concentrations and strain diversity were analysed in various oyster tissues stored overnight at 26°C that were subsequently divided into two treatment groups: one received post-harvest processing (PHP) via individual quick freeze and one was stored on ice. Vibrio vulnificus densities were 10-fold lower in all PHP-treated tissues compared with untreated tissues. Genetic diversity of V. vulnificus was assessed by BOX-PCR genotyping and was high in all oyster tissues, but was significantly lower in untreated compared with PHP-treated oysters. BOX-PCR discriminated strains into BOX-C (clinical-associated) and BOX-E (environmental-associated) types based on a 1.1kb DNA band, which correlated well (83% agreement) with 16S rRNA (A/B) typing. A significantly higher proportion of BOX-C isolates were recovered from PHP oysters compared with untreated oysters (24% of all isolates versus 12%) suggesting that BOX-C strains may be more resistant to treatment. These results reveal highly diverse populations of V. vulnificus in oysters with different responses to PHP, emphasizing the need to better understand the organism's ecology and population genetics to optimize food safety practices.