This study focuses on Vibrio parahaemolyticus strains L2171 and L2181 isolated from a Penaeus vannamei shrimp hatchery. Both strains carry the pVA plasmid harboring the PirAB genes encoding the binary PirAB toxins that cause the acute hepatopancreatic necrosis disease AHPND in cultured shrimp. The strains also harbor multidrug resistance (MDR) and a repertoire of virulence factor genes. Our goal was to determine their complete genome sequences and perform a comprehensive analysis of their genetic characteristics. The results contribute to a better understanding of V. parahaemolyticus and its role as a pathogen in a commercially important species such as farmed shrimp, providing valuable insights for disease management in aquaculture.