Potentiality of the use of tuna byproducts as a fish-meal replacement on Nile tilapia (Oreochromis niloticus) was examined for 84 weeks by tracking the concentrations of cadmium and mercury in the internal organs, muscles and fish whole body through generation including their immature eggs and their larvae. The results confirmed that the tuna byproducts can be used as a fish-meal substitute in tilapia aquaculture, because their acceptable ranges for cadmium and mercury consequently did not exceed the food safety values (both < 0.5 mg kg−1), despite their proportional increases in the fish body. The use of tuna byproducts as a protein source is expected to reduce the cost of feed with other fishmeal substitutes in tilapia aquaculture. However, fish (flounder) indiscriminately consuming tuna byproduct feed were prohibited and recalls of sales were issued by the government (July 2018, Republic of Korea), as the threshold for mercury in the fish bodies had been exceeded (0.6–0.8 mg kg−1). Further study of the use of tuna byproducts as fishmeal replacements for other species in aquaculture is needed, as concentration ratios can vary depending on the species.