The combined result of the mechanisms of sex determination and sex differentiation is the sex ratio of a population. Because sex-related growth dimorphism in fish is quite common, sex ratios influence population reproductive capacity and contribute to size variation and growth patterns before and after sexual maturation. This may have practical consequences for aquaculture and explains the interest in sex control to favor the sex with superior growth, better food conversion efficiency, later sexual maturation, or to prevent reproduction if both sexes mature before harvest. This review concentrates on recent research using molecular biology tools to broaden our understanding of the different aspects related to fish sex differentiation, both in modal fish species and economically important species. The contribution of genomics to this field is mainly through the use of microarrays for the analysis of the transcriptome, to identify expression signatures associated with the development of a particular phenotype, or genes involved in the process of sex differentiation, both under normal conditions and after exposure to a particular natural or aquaculture environment.