The use of molecular genetic markers to address questions related to aquaculture management has steadily grown over the last two decades. These markers can provide valuable information for various aspects of aquaculture practice, such as: (i) genetic identification and discrimination of aquaculture stocks; (ii) monitoring of inbreeding or other changes in the genetic composition of the stocks that may result from such phenomena as breeding programmes, founder events and genetic drift; (iii) comparison between hatchery and wild stocks; (iv) assessment of the impact on natural populations of escaped or released cultured fish; (v) assignment of progeny to parents through genetic tags, so that animals from different families can be reared together in breeding programmes; (vi) identification of marker genetic loci associated with quantitative trait loci (QTL) and use of these markers in selection programmes (marker assisted selection); and (vii) assessment of successful implementation of genetic manipulations such as induction of polyploidy and gynogenesis. The application of genetic markers to aquaculture management is demonstrated here by the analysis of genetic variability in cultivated and wild populations of gilthead sea bream (Sparus aurata).