ObjectiveTo evaluate the effects of drinking chlorinated water on the intestinal flora of rats and mice and to explore differences in the intestinal microecological responses of model animals to chlorine stimulation in chlorinated drinking water systems. MethodsSix 8-week-old male SD rats and six 8-week-old male C57BL/6J mice were acclimated for 5 days. Subsequently, the drinking water for both rats and mice was changed from pure water to water containing free chlorine at a concentration of 25.4–32.4 nmol/L. The intervention lasted for 8 weeks, during which all animals were fed the same diet. Fecal samples were collected before the intervention (week 0, as the control group) and on the last day of week 3 and week 8 (as the chlorinated water group), and microbial composition was analyzed by 16S rRNA sequencing, including α diversity (Chao1 and Shannon indices), β diversity [principal component analysis (PCA)], and linear discriminant analysis effect size (LEfSe) analysis. ResultsAfter 3 weeks of intervention, α diversity of the intestinal flora in both rats and mice in the chlorinated water group was significantly lower than that in the control group (P < 0.01). After 8 weeks of intervention, no significant difference in α diversity was observed between rats in the chlorinated water group and those in the control group, whereas α diversity in mice remained significantly lower than that in the control group (P < 0.01). β diversity analysis showed significant alterations in microbial structure in the chlorinated water group. LEfSe analysis indicated that, compared with the control group, the abundances of Bacteroides and Ruminococcus were significantly reduced in the chlorinated water group, and microbial disturbance was more pronounced in mice [linear discriminant analysis (LDA) > 4.0], with a greater decrease in microbial diversity and a larger number of differentially abundant genera. ConclusionConsumption of chlorinated water can alter the diversity and structure of the intestinal flora in both rats and mice, with mice being more sensitive to this exposure. These findings suggest that the potential effects of chlorine on gut microecology should be considered in drinking water management and model selection for animal experiments.