This study from January to December 2018 was the rst initiative of a Port Baseline Survey (PBS) aimed at assessing the impact of biological invasions in harbours of the Gulf of Gabès (GG). A total of 12 shing and industrial harbours were seasonally prospected during 2018. A total of 174 macrobenthos taxa were recorded, belonging to eight zoological groups, with a dominance of crustaceans (32%), molluscs (31%) and polychaetes (20%). Among these taxa, 57 were Non-Indigenous Species (NIS) for Tunisian waters, while 27 species were recorded for the rst time in GG harbours and three decapods ( Dyspanopeus sayi, Hippolyte prideauxiana and Pilumnus minutus ) and one amphipod ( Hamimaera hamigera ) were newly recorded from Tunisian waters. Two main categories of harbours are distinguished according to their macrobenthic communities and environmental features (essentially edaphic factors). The industrial harbours yield higher numbers of species and abundance of NIS than the shing ports. The ALEX metric is used to evaluate the biological invasion status of the Gulf of Gabès harbours, showing that their status ranges from unaffected in shing harbours to extremely affected in industrial harbours. Three biotic indices (AMBI, BO2A and BENTIX) are applied to assess the ecological status of harbours, which varies from moderate to good. ALEX and the other biotic indices are signi cantly correlated with harbour characteristics, maritime tra c and edaphic factors (organic matter and chemical contamination). The present study gives an overview of all available benthic data, the impact of biological invasions and the ecological quality status of harbours in the Gulf of Gabès. The results could be considered as providing important baseline data for the implementation of environmental policies and management plans in the future.