The objective of this research is to examine the similarities between port traffic structure and economic structure of French port cities. Such an exercise is challenged by the core-periphery pattern of the French economy favouring transhipment. Based on the combination of Automated Identification System (AIS) data and employment data, it performs complementary analyses of the mutual specialization between ports and cities. Main results show that while larger cities handle more diversified traffic, the cross-specialization is blurred by the complexity of trade networks and supply chains. We then propose a novel methodology whereby the spatial unit of analysis is enlarged according to the type and volume of port traffic, thus considerably improving the statistical significance and economic meaningfulness of the observed linkages.