Aims: We analysed the genetic divergence in the pandemic new O3: K6 and phylogenetically related ( new O3: K6-like) strains and compare these two groups in terms of virulence and other biological traits. Methods and Results: A total of 160 new O3: K6, new O3: K6-like and other strains of Vibrio parahaemolyticus isolated in Taiwan and other countries were collected and their clonal relationships analysed using SfiI-pulsed- field gel electrophoresis. All of the new O3: K6 and new O3: K6- like strains were grouped in cluster I with five new patterns identified. A O6: K18 strain was identified as a new member of the new O3: K6- like strains in addition to O4: K68, O1: KUT and O1: K25 strains. All of the lipopolysaccharide preparations of the selected strains exhibited closely spaced quadruplet banding patterns with similar mobility. The two groups of strains exhibited 100% sequence identity in the internal sequences of the toxR and laf genes, and also displayed similar virulence properties as determined with a suckling mouse model. Conclusions: The new O3: K6 and new O3: K6- like strains were highly similar in virulence and in several other phenotypical and genotypical traits. Significance and Impact of the Study: This work demonstrated the spread and divergence of the pandemic and related clone of V. parahaemolyticus with similar virulence.