Traceability of seafood has become crucial with market globalization and consumer's awareness. The present study used PCR-DGGE and 454 pyrosequencing to assess if bacterial communities fingerprint associated to seabass (Dicentrarchus labrax) skin mucus can be used to discriminate the geographic origin of fishes cultured in three semi-intensive fish farms. PCR-DGGE and pyrosequencing results were congruent and suggested that this molecular approach has the potential to trace fish farms with a spatial resolution <500 m. Pyrosequencing results provided a detailed insight into the bacterial community composition of seabass skin mucus and revealed the existence of a core of bacterial communities within family Pseudomonadaceae and Rhodobacteraceae. This approach also allowed to recognized key OTUs that are potentially relevant to discriminate the geographic origin of the fish being surveyed. Overall, the present study increased our knowledge on farmed seabass microbiome and demonstrated that specific and unique bacterial taxa can act as natural signatures that allow us to trace fish to its respective geographic origin. Our study provides valuable clues that should be more investigated in future studies as a way to fulfill current traceability needs in the global trade of seafood.