Abstract Introduction The purpose of this study was to assess enrichments in stable carbon and nitrogen isotopes (δ13C and δ15N) in brown-marbled groupers (Epinephelus fuscoguttatus), a marine fish that has been widely used in aquaculture. Stable isotope analysis has been used to evaluate dietary sources and the trophic position of fish. There is the need to better understand the pattern of isotope enrichment between consumers and diets under laboratory conditions. Methods We studied the changes in stable carbon and nitrogen isotopes of juvenile brown-marbled groupers during a feeding experiment in 2009. Fish were grown in aquaria and fed a sole source of protein for 56 days and analyzed for δ13C and δ15N ratios in whole fish, muscle, and liver tissues. Results At the end of the 56-day feeding experiment, fish grew to an average of 55.6 g from an average of 22.5 g. Compared to the dietary isotope compositions, whole fish and muscle tissues of the juvenile groupers were enriched in δ13C by 1.6 and 0.5‰, while the liver was depleted by 1.3‰. The δ15N enrichments were 1.6‰ for whole fish, 1.3‰ for muscle, and 1.0‰ for liver. Except for liver, δ15N isotope values increased significantly with time. Conclusions The small change in δ13C between the diet and fish suggests that little isotope alteration is occurring during the assimilation of dietary carbon. This provides a basis for estimates of the importance of different sources of dietary components when contrasted with the isotope values from a formulated diet with known isotope values of the different components. The smaller than expected δ15N enrichment in all tissue suggests that isotope values from a wild fish sample may not always reach isotope equilibrium with the current diet, and an inference about recent dietary sources and an estimate of the consumer’s trophic position should be evaluated with caution.