Genome architecture of soles has been intensively explored in the last years, particularly with the arrival of Next Generation Sequencing (NGS) techniques. Hence, a large amount of transcriptomic and genomic data has been generated facilitating the identification of molecular markers and the development of expression tools required to decipher the molecular mechanisms that govern important traits such as growth, development or reproduction and the effects of diets, micronutrients or immunostimulants. In this chapter, the main features of the transcriptome, genome and epigenome of S. senegalensis and S. solea, when available, are described. Moreover, the main uses and applications of these resources to design novel expression tools in Senegalese sole, with some examples will be reviewed. Finally, due to the importance of these species in aquaculture, main advances in molecular markers and the implementation of genetic breeding programs will be discussed emphasising in the current bottlenecks, tools, methodologies and strategies designed for an optimal management of genetic resources in the industry.