High and sudden mortalities of Penaeus vannamei post-larvae (PL1–PL5) in Latin American commercial hatcheries, occasionally reaching 100% within two hours, were investigated using microbiological, molecular, and histopathological approaches. Historical samples collected from 22 tanks across six hatcheries between 2015 and 2021 revealed that diseased larvae suffered from a condition termed post-larvae acute hepatopancreatic necrosis disease (PL-AHPND). Histopathological examination of affected post-larvae showed massive sloughing and detachment of hepatopancreatic tubule epithelial cells, loss of tissue architecture, presence of cell debris in the tubular and gut lumen, and absence of the peritrophic membrane without classic melanosis. Disease progression occurred in two phases: an early hemocytic infiltration phase followed by a rapid acute-terminal necrosis phase. Molecular testing using AP4 nested PCR confirmed the presence of VpPirAB toxin genes in isolated Vibrio strains, including V. parahaemolyticus and V. alginolyticus. Toxicity bioassays demonstrated higher virulence in early stages (PL1–2; 24-h LC50 of 6.3 × 10³ CFU/mL at 30 °C). Comprehensive diagnosis combining histopathology and PCR is critical to differentiate PL-AHPND from other larval pathogens.