S. aurata is a marine fish living along the Atlantic coasts of Europe and the Mediterranean Sea. It is an important food species so its production reached 128,943 t in European aquaculture in 2008. However, little is known about its biology, in particular the effective and census sizes, distribution, spawning grounds, and behavior. Also, the species subdivision still needs to be clarified. In this review, studies related to gilthead sea bream populations and problems with the clarification of gilthead seabream population structure in hatchery and wild were reviewed. Also, it was intensified on potential research areas, having importance in the determination of population structure of gilthead seabream such as morphology and behavior in hatchery and wild. Determination of the genetic structure of S. aurata populations based on behavior and morphology will not only contribute greatly to the biological clarification of the species but also will help the development strategy for the conservation of natural stocks (e.g., protecting the stopover points) and the determination of reference stocks, which is important for the culture of gilthead seabream to use in the genetic improvement programs.