Two Vibrio parahaemolyticus virulence genes, pirAvp and pirBvp, are known to encode a binary photorhabdus insect-related (Pir) toxin that causes acute hepatopancreatic necrosis disease (AHPND) in shrimp. These genes are flanked with repeats of a mobile element (insertion sequence) in a large plasmid. This insertion sequence is closely (92%) related to the known insertion sequence ISVal1. The pirABvp genes and the flanking ISVal1 forms a 5535-bp composite transposon, designated Tn6264. There are pirABvp gene deletions in some strains of V. parahaemolyticus. During 2013–2016, we found 2 types of pirABvp deletion mutants from AHPND-affected farms. The type I mutants included 3 strains with deletions (4.4-kb or 6.0-kb) of entire pirABvp genes and the downstream ISVal1, and these mutants were named pirABvp(‐). The type II mutants included 3 strains with smaller deletions (1.5-kb or 1.6-kb) including a pirAvp gene and a partial pirBvp gene, and were named pirAvp(‐). In laboratory bioassays, these were not pathogenic to shrimp confirming that both pirAvp and pirBvp are required for AHPND pathogenicity. During 2016, we also isolated 4 V. campbellii strains carrying pirABvp genes from diseased shrimp. These V. campbellii stains were found, through laboratory bioassays and histological evaluation, to cause AHPND. •A composite transposon, named Tn6264, consists of pirABvp genes and the flanking insertion sequence (ISVal1), is associated with AHPND of shrimp.•Two types of pirABvp deletion mutants of V. parahaemolyticus were found in the AHPND-affected farms.•The type I mutants, named pirABvp(-), have deletions (4.4-kb or 6.0-kb) of entire pirABvp genes and the downstream ISVal1.•The type II mutants, named pirAvp(-), have smaller deletions (1.5-kb or 1.6-kb) of pirAvp and including a partial pirBvp.•V. campbellii strains carrying pirABvp genes were found, through laboratory bioassays and histologicial evaluation, to cause AHPND.