Abstract: Fermented cottonseed meal (FCSM) is a high-quality plant protein ingredient with potential to replace fishmeal in feed. To evaluate the suitability of FCSM as a protein source in the diet of juvenile golden pompano (Trachinotus ovatus) and its appropriate replacement level, we had fed the juveniles with initial body mass of (12.57±0.25) g for seven weeks by five diets to replace 0% (Control group), 25%, 50% and 100% of fishmeal by FCSM, and the fish meal in reference diet was 35%. Then we investigated the effects of FCSM replacement of fishmeal on the survival, growth, feed utilization performance and intestinal microflora of the juveniles. The results show that the survival, growth, feed efficiency, dietary protein and lipid deposition rates were lower in FCSM treatments compared with those in reference diet, while the differences between 25%, 50% replacement groups and the reference diet were not significant (P>0.05). However, the liver antioxidant system was stimulated, and the activities of total superoxide dismutase (T-SOD) and catalase (CAT) in 75%−100% replacement groups were higher than those in the control group. In addition, the liver hematoxylin-eosin-stained sections show that the cellular vacuolation phenomenon was aggravated. The contents of total protein, albumin and globulin in serum in 100% replacement group were reduced, and the protein synthesis capacity of liver might be impaired. High-level replacement of fish meal by FCSM affected the composition of intestinal flora, with the abundance of beneficial bacteria decreasing and that of harmful bacteria increasing. Taking into account both growth performance and fish health, it is recommended to replace fish meal with 25% FCSM in the diet for T. ovatus.