The exceptionally fast growth that fish experience after periods of fasting has been called “compensatory growth” or “catch up” growth. This phenomenon, reported in a wide range of fish species, has been studied in intensive aquaculture as a means of enhancing feed conversion efficiency, but the mechanisms implicated are complex and not yet fully understood. Our research focuses on identifying candidate genes whose expression contributes to the compensatory growth induced by refeeding in sea bass (Dicentrarchus labrax). As an alternative to genome sequencing for discovering genes in this teleost, we have successfully implemented a process for identifying unknown genes, assuming that a computational database resource contains orthologous sequences from phylogenetically related species. Following this similarity-driven molecular cloning and sequencing, we isolated several full-length sea bass cDNAs that encode for some physiologically relevant proteins in this species. We have then made use of the DNA sequence data to understand the function of these genes with the aim to identify valuable molecular biomarkers influenced, either positively or negatively, by dietary manipulations. Accordingly, in this chapter, we describe the utilization of molecular cloning and functional genomics in aquacultured sea bass to generate “transcriptome-focused” information, which may enable a better understanding of the transcriptional programs that underlie compensatory growth induced by refeeding.