The balanced selective nature of protein polymorphism in fishes is reviewed, noting its diversity and association with molecular structure and size. The functional and kinetic differences between allelic variants are discussed for the few species within which they have been studied, and related to population size, habitat and clinal variation. Heterosis is discussed in relation to heterozygote excess and deficit in natural and in reared populations, and the nature of heterozygote advantage considered. Natural selection of protein loci is evidenced in changes of allele frequency with age, with experience of environmental extremes (heated effluents), and in culture. Finally, it is argued that protein polymorphism has a primarily adaptive nature, arising through selection pressures rather than through genetic drift.