The lateral line of aquaculture fishes has rarely been studied although it is a very important anatomical organ that could serve as an inexpensive and easy tool to distinguish farmed from wild individuals. In the present study, lateral line deformities were examined in both wild and farmed sea bass (Dicentrarchus labrax) and sea bream (Sparus aurata) specimens to try to detail all possible differences between them. In order to do so, the morphology of the trunk lateral line in wild and farmed adults was examined whereby two major deformities were observed in both species: the ‘scale pocket’ deformity (14–40% incidence in all groups) where the specialized scales are missing but the canal underneath is present and the scale print is obvious, and the ‘somatic scales’ deformity (14–56% incidence in farmed individuals only) where the missing lateral line is covered with normal somatic scales. Histological examination confirmed the macroscopic observations in that the lateral line mechanism was present – although damaged – beneath the scale pocket deformity and completely absent beneath the somatic scales deformity. It is argued that the scale pocket deformity is a result of an accident during the life of the fish whereas the somatic scales deformity is an actual deformity in development.