The main purpose of this study was to find the optimal cochineal dye concentration and treatment time for marking Japanese smelt (also known as Wakasagi) Hypomesus nipponensis, more specifically their eggs, by understanding the mechanisms that determine survival rates and mark quality. Eggs were immersed in a range of cochineal dye concentrations (40-100 g/L) at varying intervals (6-72 h). Following that, mark quality was evaluated according to fluorescence intensity by examining the marked otolith of the larvae. The statistical model selection indicated that the interaction between the cochineal dye concentrations and immersion intervals (g/L × h) had a negative effect on survival such that at low concentrations survival decreased with increasing immersion time but at high concentrations survival was relatively low at all of the immersion times. On the other hand, the results of evaluating the marked otoliths indicated that mark quality improved with increases in concentration and immersion time individually. These results suggest that there is a trade-off between mark quality and survival of Japanese smelt when using a cochineal dye solution. Combining the results of the survival rate and mark-quality experiments, the cochineal dye marking conditions with both high survival rates and high fluorescence intensity are 60 g/L for 24 h, 40 g/L for 48 h, and 40 g/L for 36 h.