Egg quality can be defined as the egg ability to be fertilized and subsequently develop into a normal embryo. The ability to produce large numbers of high quality eggs “on demand” is an important issue for the development of aquaculture. Egg quality is deeply influenced by environmental factors and husbandry practices. Egg quality is a difficult to measure phenotype and is therefore not currently included in most selection programs.Automatic phenotyping of early embryonic success (i.e., mortalities and deformities) is a challenge. Our understanding of what makes a good egg remains incomplete despite the identification of key molecular mechanisms participating in egg quality. The identification of robust and generic (i.e., shared by evolutionary distant species) molecular markers of egg quality is a challenge for the future of aquaculture.