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The aim of this study was to evaluate the effect of enzymolytic soybean meal (ESBM) on antioxidant capacity, intestinal morphology and caecal microbiota in Rex rabbits. One-hundred-twenty 40-day-old healthy Rex rabbits were randomly divided into four groups with thirty replicates in each group and one rabbit per replicate. The control group was fed the basal diet and the ESBM treated groups (T1, T2 and T3) were fed 0.5%, 1% and 1.5% ESBM instead of the equivalent amount of soybean meal (SBM) in the basal diet, respectively. The study lasted 61 days, including a pre-feeding period of 5 days and a formal trial period of 56 days. Compared with the control group, the activity of superoxide dismutase and glutathione peroxidase in the liver, as well as total antioxidant capacity were significantly increased in the T3 group (p < 0.05). The malondialdehyde concentrations in the liver and jejunum were significantly decreased in the T1 group (p < 0.05). There were no significant differences in the antioxidant capacity of jejunum, intestinal morphology index and intestinal pH among all groups (p > 0.05). Compared with the control group, the relative abundance of Ruminococcaceae_UCG-013 was increased significantly in both T2 and T3 groups (p < 0.05), and the relative abundance of Ruminococcaceae_unclassified was decreased significantly in all treatment groups (p < 0.05). In conclusion, the replacement of equivalent amounts of SBM with ESBM in the diet of Rex rabbits can increase the antioxidant capacity of the liver and improve the caecal microbiota, and the optimal replacement level was 1.5%. Enzymolytic soybean meal (ESBM) increased the liver antioxidant capacity of Rex rabbits. ESBM improved the caecal microbiota of Rex rabbits. Effects of ESBM on the intestinal morphology and pH of Rex rabbits were evaluated. [ABSTRACT FROM AUTHOR]