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This paper reports the features of a web-based multi-agent system (MAS) which aims at supporting electronic data interchange (EDI) among seaport operators and providing interoperability among ports. The MAS architecture here proposed performs process automation, data integration, security and quality of managed information better than a tradional client-server. The case study is represented by the italian port of Taranto and three greek ports (Igoumenitsa, Salonica and Kavala). This paper draws on a work in progress within INTERREG III ARCHIMED PROGRAMME for New.Ton. Project, a project co-financed by the European regional development fund (ERDF).