The review discusses the interactions between host immunity and intestinal microorganisms in fish, focusing on recent advances in zebrafish (Danio rerio). It highlights how fish immunity senses and shapes the intestinal microbiota, and how intestinal microbes tune host immunity. Key points include the role of pattern recognition receptors (PRRs) such as toll-like receptors (TLRs) and nucleotide-binding oligomerization domain 2 (NOD2) in sensing and responding to microbial components. The review also covers the impact of host immunity on intestinal microbiota composition, emphasizing the role of secretory immunoglobulin A (sIgA) and mucosal IgT in maintaining intestinal homeostasis. Additionally, it explores how host-derived beneficial microbes regulate fish immune functions and shape microbial structures, enhancing disease resistance and improving overall health. The review concludes by discussing the potential of probiotics in promoting healthy fish physiology through gut microbiota regulation and immune system modulation.The review discusses the interactions between host immunity and intestinal microorganisms in fish, focusing on recent advances in zebrafish (Danio rerio). It highlights how fish immunity senses and shapes the intestinal microbiota, and how intestinal microbes tune host immunity. Key points include the role of pattern recognition receptors (PRRs) such as toll-like receptors (TLRs) and nucleotide-binding oligomerization domain 2 (NOD2) in sensing and responding to microbial components. The review also covers the impact of host immunity on intestinal microbiota composition, emphasizing the role of secretory immunoglobulin A (sIgA) and mucosal IgT in maintaining intestinal homeostasis. Additionally, it explores how host-derived beneficial microbes regulate fish immune functions and shape microbial structures, enhancing disease resistance and improving overall health. The review concludes by discussing the potential of probiotics in promoting healthy fish physiology through gut microbiota regulation and immune system modulation.