Sexual dimorphism is one of the most pervasive and diverse features of animal morphology, physiology, and behavior. Despite the generality of the phenomenon itself, the mechanisms how sex is determined are very different among various organismic groups and have independently evolved repeatedly across metazoans and the underlying molecular pathways can change quickly during evolution. While phylogenetic studies suggest that the downstream “business” ends of sex-determining pathways do tend to be more stable than the triggering mechanisms at the top, the main questions are: (i) how similar are the downstream genes networks that respond to these triggers and actually do the work? (ii) Did sex determination arise several times with different regulatory mechanisms converging by recruiting conserved key effectors, or (iii) is it an ancient process with little surviving evidence of ancestral genes? In stark contrast to birds and mammals, where the whole group has the same sex determination mechanisms, but similar to amphibians and reptiles, the diversity of sex determination mechanisms is especially obvious in fish, where within groups of closely related species a wide spectrum of different systems can be found. To better understand the biological meaning of such diversity and the underlying mechanisms driving sex chromosome evolution we attempt to decipher the molecular basis of the primary sex determination mechanisms and the structure and genetic organization of sex chromosomes across a broad diversity (>40 species) of ray-finned fishes representing the major branches of the fish tree of life using a combination of genome wide approaches and functional genomics.In details, this plasticity is particularly evident in species of the genus Oryzias, which includes the medaka fish. Here, the master male sex determination gene (Dmrt1bY) is known, but this gene is absent from closely related species. Medaka is a well-suited laboratory fish that offers genomic resources and transgenic technologies for functional studies on the molecular basis of sexual determination. Using the medaka fish as a major model organism emphasis will be given on how dmrt1bY was born in that particular context of comparative evolution (“evo-devo”).