Acute hepatopancreatic necrosis disease (AHPND) is caused by Vibrio parahaemolyticus containing toxins. The toxins are controlled by the genes pirA and pirB. The PirAvp/PirBvp toxin induces cell death in the shrimp’s hepatopancreas but not in the stomach or other organs. It looks pretty likely that these putative PirAvp/PirBvp receptors will be found exclusively in the hepatopancreas membrane. Here we used protein homology modeling and protein-protein docking approaches to understand the cytotoxic mechanisms of PirAvp/PirBvp toxins, which is likely to be essential for AHPND research and agricultural applications. We selected aminopeptidase N (APN)- and alkaline phosphatase (ALP) as candidate cellular receptors for modeling cytotoxic mechanisms of V. parahaemolyticus PirAvp/PirBvp toxins. For this end, we chose Penaeus vannamei shrimps cytosol aminopeptidase cysteinyl glycine-S-conjugate dipeptidase (UniProtKB A0A423TDZ4_PENVA) as well as Penaeus vannamei shrimps alkaline phosphatase (UniProtKB A0A3R7PII5_PENVA) as cellular receptors for PirAvp/PirBvp, B. thuringiensis Cry, and Cry6Aa toxins. The PDB codes 3X0T and 3X0U for PirAvp and PirBvp and 5KUC and 1JI6 for Cry6Aa and Cry toxins were used for protein-protein docking experiments. The fasta and pdb files for Penaeus vannamei shrimps APN and ALP were downloaded from the UniProt database. The protein homology modeling was carried out by using SWISS-MODEL algorithms for template search (BLAST and HHblits against the template library), model building (ProMod3 coordinates which are conserved between the target and the template), and model quality estimation (QMEAN scoring function). For protein-protein docking, ezCADD and Patchdock algorithms were used, and Discovery Studio Visualizer and PyMOL software analyzed the results.