The shrimp industry has historically been affected by viral and bacterial diseases. One of the most recent emerging diseases is the Acute Hepatopancreatic Necrosis Disease (AHPND), which causes severe mortality. Despite its significance to both sanitation and economics, little is known about the molecular response of shrimp to this disease. Here, we present the cellular and transcriptomic responses ofLitopenaeus vannameiexposed to twoVibrio parahaemolyticusstrains for 98h, wherein one is non-pathogenic (VpN) and the other causes AHPND (VpP). Exposure to VpN strain resulted in minor alterations in hepatopancreas morphology, including reductions in the size of R and B cells as well as detachments of small epithelial cells from 72 h onwards. On the other hand, exposure to VpP strain is characterized by acute detachment of epithelial cell from the hepatopancreatic tubules and infiltration of hemocytes in the inter-tubular spaces. At the end of exposure, RNA-Seq analysis revealed functional enrichment in biological processes, such as thetoll3receptor signaling pathway, apoptotic processes, and production of molecular mediators involved in the inflammatory response of shrimp exposed to VpN treatment. The biological processes identified in the VpP treatment include superoxide anion metabolism, innate immune response, antimicrobial humoral response, andtoll3receptor signaling pathway. Furthermore, KEGG enrichment analysis revealed metabolic pathways associated with survival, cell adhesion, and reactive oxygen species, among others, for shrimp that were exposed to VpP. Our study proves the differential immune responses to two strains ofV. parahaemolyticus,one pathogenic and the other nonpathogenic, enlarges our knowledge on the evolution of AHPND inL. vannamei, and uncovers unique perspectives on establishing genomic resources that may function as a groundwork for detecting probable molecular markers linked to the immune system in shrimp.