The development of sustainable aquaculture models requires an increasing knowledge of hatchery production practices. This preliminary study has aimed at investigating the domestication process in the European sea bass, Dicentrarchus labrax. Genetic variability and frequencies of anatomical abnormalities were inspected in five hatcheries and in one sample of wild sea bass juveniles. Gene-enzyme analysis (carried out through starch gel electrophoresis on about 300 individuals) revealed low genetic distances among groups, and allelic and genotypic frequency shifts in the hatchery groups when compared to the wild one. The analysis of differences in meristic counts and physical anomaly types and frequencies (evaluated on more than 430 juveniles) revealed a wide morphological variation among the hatchery groups and also between these and the wild group, with some hatchery-specific trends.