The traits of cultured fish must continually be genetically improved to supply high-quality animal protein for human consumption. Economically important fish traits are controlled by multiple gene quantitative trait loci (QTL), most of which have minor effects, but a few genes may have major effects useful for molecular breeding. In this review, we chose relevant studies on some of the most intensively cultured fish and concisely summarize progress on identifying and verifying QTLs for such traits as growth, disease and stress resistance and sex in recent decades. The potential applications of these major-effect genes and their associated markers in marker-assisted selection and molecular breeding, as well as future research directions are also discussed. These genetic and genomic analyses will be valuable for elucidating the mechanisms modulating economically important traits and to establish more effective molecular breeding techniques in fish.