The demand and preference for alternative ferry transport hubs are discussed using the region of the Aegean Archipelago as a case study. A complex network of connections among the islands and to the Greek peninsula serves the needs of tourism, transportation of goods and services, and islanders traveling to and from the mainland.However, this system has shortcomings; in particular, interconnections for many islands are only possible via the mainland ports of Greece. Interconnectivity among the islands is important for the economic, social, and territorial cohesion of the archipelago as well as to meet the needs of tourism. This study looks into passengers’ acceptance of two alternative minor island connection ports that would increase remote island connectivity. Econometric tools and a stated preferences survey were used to assess the acceptance of minor island hubs versus the existing major mainland maritime hubs. Discrete choice models were estimated in which the attributes of the alternatives include travel times, waiting times at the interchange hubs, fares, and selected socioeconomic parameters of the respondents. The results show a positive trend in favor of the proposed minor hub system. In conclusion, this innovative methodology could be used for policy testing and transferable to similar archipelagic regions.