Identifying the provenance of seafood is critical to combat commercial fraud, enforce food safety regulations and ensure consumers confidence. Hence, the current study aimed to determine if the bacterial composition present in the digestive gland of M. galloprovincialis mussels could be used as traceability approach to discriminate their geographic origin. The microbiota of 160 mussels collected seasonally in 2019 from five different mussel farms located in three regions in Spain (Galicia, Basque Country and Catalonia) was characterized using 16S rRNA targeted amplicon sequencing. Results showed that the bacterial community composition/fingerprint was significantly different between harvesting locations and seasons, with the effect prompted by the origin exceeding the seasonal variability. To further evaluate the stability and potential of this traceability approach, the bacterial fingerprint of 20 new individuals collected from the Basque Country in autumn 2020, which had been independently processed, sequenced and analysed, were compared to the profiles obtained in 2019. Results showed that mussels collected from the Basque Country in two consecutive years cluster together, even matching the season of harvesting. Our findings support that this methodological approach has the potential to trace the geographical origin of unprocessed mussels and could have potential uses in seafood traceability and food safety.