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Coastal areas around the world are threatened by an accelerated sea level rise (SLR), storm surges and coastal flooding related to climate change. These threats, together with the land use pattern of coastal areas, could create a dangerous mix for coastal communities and could result in major socio-economic and environmental consequences. Apart from human settlements, seaports are likely to be most vulnerable to climate change because they are located at areas exposed to SLR and storm surges or at mouths of rivers susceptible to flooding. To remain efficient and resilient, seaports must anticipate the impacts of climate change and proactively prepare for SLR, increased flooding, and more frequent extreme storm events. This paper presents the analytical and empirical aspects of an integrated vulnerability index (VI) for small raft harbours based on the methodology of the IPCC for coastal vulnerability assessment. Six corresponding steps are adopted to assess the fishing ports VI (VIP-F) considering geophysical and socio-economic parameters. The proposed index is applied to 47 fishing boats and small commercial harbours of Lesvos, Greece. The proposed methodology can be adapted for assessing the vulnerability of major ports.