We have cytogenetically characterized a hatchery stock of gilthead seabream, Sparus aurata. The study included larvae, juveniles and adults. In S. aurata (diploid chromosome number 2n = 48), a pair of NORs is located at the ends of the short arms of the first submetacentric pair of chromosomes. In this stock we discovered a polymorphism which affects the NORs, and, by means of several cytogenetic and molecular techniques, we demonstrate that this polymorphism is due to the complete deletion of one of the two NORs in a high number of individuals. The significance of these cytogenetic characteristics for this species are discussed since they may be the source of aquaculture problems.