Large quantity of eggs fail to be fertilized and many of fertilized eggs are unable to hatch in the eel, Anguilla japonica. Larvae of eel absorb egg yolk up to 8 days after hatching but the majority of hatched larvae die before they reach the stage of first feeding in this species. Genes of key enzymes for yolk processing (cathepsin B, D, L and lipoprotein lipase - abbreviated as ctsb, ctsd, ctsl and lpl, respectively) could be associated with egg quality. In this study, we investigated differences in the expression of these genes between floating eggs and sinking eggs, and also the relationship between the gene expressions of the enzymes and fertilization rates in the fertilized eggs obtained from artificially matured female eels. Expressions of yolk processing enzyme genes did not show significant difference between floating and sinking egg groups. Expression of ctsb decreased when fertilization rate was high. Expression of ctsd, ctsl and lpl, however, did not show any significant differences. These results suggest that ctsb expression could be an indicator of egg quality, and that some proteins prone to be digested by ctsb could be very important in the process of fertilization and normal cleavage in this species. Further study should identify these critical proteins to improve our understanding on the quality of fish eggs.