Abstract: Clarifying the immune response mechanisms and epigenetic regulation characteristics of Penaeus monodon in response to bacterial infections can provide important theoretical support for disease control strategies. Through in vivo injection of Gram-negative Vibrio parahaemolyticus, Gram-positive Enterococcus faecalis, and PBS (Control), we investigated the effects of these bacteria on histology, innate immunity, and DNA methylation levels in P. monodon. Analyses were performed using hepatopancreas and gill tissue section observation along with quantitative real-time PCR (qRT-PCR). HE staining results reveal that V. parahaemolyticus infection caused the shedding of epithelial cells in the hepatopancreatic tubules and shrinkage of gill filaments. In contrast, after injection with E. faecalis, necrosis occurred in the hepatopancreatic tubular cells, and the gill tissues frequently exhibited edema and hemorrhage. Quantitative real-time PCR results show that both V. parahaemolyticus and E. faecalis significantly upregulated the expression of the antimicrobial peptide gene (Crustin) and heat shock protein 70 gene (Hsp70) after stimulation. Additionally, lipopolysaccharide-β-1,3-glucan-binding protein (LGBP) was significantly upregulated in gill tissues, while fatty acid-binding protein gene (Fabp) expression was significantly elevated in hepatopancreas tissues. Both bacterial infections significantly increased the expression levels of DNA methylation-related genes, including methyl-CpG-binding domain protein 2 (MBD2), ubiquitin-like with PHD and RING finger domains 1 (UHRF1), and DNA methyltransferase 2 (DNMT2), in hepatopancreas and gill tissues, with a more pronounced effect observed with V. parahaemolyticus stimulation. The findings demonstrate that both immune-related genes and DNA methylation-associated genes in P. monodon are significantly up-regulated upon infection by V. parahaemolyticus and pathogenic E. faecalis, confirming their crucial roles in anti-infection defense through modulation of host physiological functions.