Sanguinarine (SAG) is an alkaloid derived from the root of Sanguinaria canadensis with demonstrated anti-inflammatory, antioxidant, and antimicrobial properties. SAG is routinely used in animal feed as an alternative to antibiotics. However, its effect on intestinal microbiota in fish has not been clarified. Herein, we evaluated the effect of SAG on immune response, digestive enzyme activity, intestinal histology, and microbiota in Koi carp to gain a better understanding of the intestinal microbes. Three hundred fish were randomly assigned to four treatment groups consisting of basal diet alone or basal diet supplemented with three doses of SAG (50, 150, or 450 mg/kg). Blood was collected at the end of the feeding periods from 36 fish (n = 9 per treatment) and analyzed for serum parameters. Intestinal samples were collected to evaluate digestive enzyme activity, intestinal histology, mRNA expression of cytokines and bacterial community. Then remaining fish (n = 66 per treatment) were then challenged with exposure to Aeromonas hydrophila (A. hydrophila) to assess cumulative survival. The results indicated that dietary SAG decreased serum interleukin (IL)-1β in SAG-50 mg/kg (P = .0045), and IL-6 in SAG-50 mg/kg and SAG-150 mg/kg (P = .0021). The level of lysozyme (P < .0001), complement C3 (P = .0013) and glutathione peroxidase (GPx) (P < .0001) increased in all SAG-treated groups. The level of superoxide dismutase activity (SOD) increased in SAG-50 mg/kg (P < .0001), but malondialdehyde (MDA) decreased in SAG-50 mg/kg and SAG-150 mg/kg (P < .0001). Lipase activity was significantly decreased in SAG-50 mg/kg (P < .0001). No difference was observed in intestinal villus height, crypt depth, muscle thickness, and ratio of villus height to crypt depth (V/C ratio) in any group. Furthermore, SAG decreased the expression of TNF-α (P < .0001) and IL-1β (P < .0001) in the intestine. The 7-day cumulative survival increased in all SAG-treated groups (P = .0029). Moreover, low dose SAG induced changes in the β-diversity of bacterial community structure (P = .050). In conclusion, dietary SAG showed anti-inflammatory and anti-oxidative effects in koi carp. SAG enhanced non-specific immunity and survival in response to A. hydrophila infection. These SAG-mediated benefits may be associated with the structure of intestinal bacterial community. •Dietary sanguinarine showed anti-inflammation and anti-oxidant effects in koi carp.•Sanguinarine enhanced innate immune response, and elevated the resistance against A. hydrophila infection.•Low dosage of sanguinarine induced changes in Beta-diversity of bacterial community structure (P = .050).•Sanguinarine-mediated benefits may be associated with the structure of intestinal bacterial community.