Background: The giant trevally, Caranx ignobilis, is a commercially important marine fish in Indonesia. This species was initially cultured in Aceh Province. Previous reports showed that charcoal has a positive effect on survival and feed utilization of the giant trevally. However, the effects of adding charcoal to the diet on gut and intestine biometrics has, to our knowledge, never been described. Methods: Four activated charcoal sources were tested in this study using a completely randomized experimental design; coconut shell charcoal, mangrove wood charcoal, rice husk charcoal, and kernel palm shell charcoal. All treatments were performed with four replications. Juvenile giant trevally (average body weight, 16.52 ± 3.12 g; and average total length, 10.26 ± 0.64 cm) were stocked into the experimental tank at a density of 15 fish per tank. The fish were fed an experimental diet twice daily at 7 AM and 5 PM ad satiation for 42 days. Results: Analysis of variance showed that adding charcoal to the diet had significant effects on the length and width of the foveola gastrica and villous intestine (P < 0.05). The greatest length and width of the foveola gastrica was recorded in fish fed an experimental diet of rice husk charcoal with average values of 311.811 ± 9.869 µm and 241.786 ± 10.394 µm, respectively. The greatest length of intestinal villous was found in fish fed the mangrove wood charcoal diet, with a value of 135.012 ± 5.147 µm, but this length was not significantly different to that in fish fed rice charcoal and kernel palm shell charcoal. However, the greatest width of intestinal villous was recorded in fish fed the control diet (without charcoal; P < 0.05). Conclusion: The optimal sizes of the foveola gastrica and villous intestine were found in fish fed an experimental diet with rice husk charcoal.