An experimental trial was conducted for 90 days to evaluate the effect of different carbon sources viz. yam and potato on growth performance of milkfish (Chanos chanos) in biofloc‐based system. Milkfish fry (average body weight of 0.66 ± 0.01 g) was stocked in biofloc treatments, yam‐based biofloc (BFY) and potato‐based biofloc (BFP), and clear water (CW) as control in triplicates. Milkfish reared in biofloc‐based units obtained significantly better (p < 0.05) performance in terms of growth, digestive enzyme activity and survival when compared to clear water control. Among the biofloc‐based treatments, the highest average body weight (11.62 ± 0.24 g), specific growth rate (3.21 ± 0.01% day−1), percentage weight gain (1688.10 ± 19.05) and survival (90.83 ± 2.01%) were found in BFY group. Similarly, the essential amino acid and non‐essential amino acid contents of biofloc and experimental fish were higher in BFY as compared to BFP. Additionally, the highest level of EPA (eicosapentaenoic acid), DHA (docosahexaenoic acid) and total n‐6 and n‐3 PUFA were found higher in BFY. Bacterial composition analysis showed that BFY treatment groups had a more diverse bacterial community than those with BFP treatment groups. This study demonstrated that biofloc‐based culture system is suitable for rearing of C. chanos fry and the most preferable type of carbon source is found to be Yam.
