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In the Mediterranean Region, habitat loss and fragmentation severely affect coastal wetlands, due to the rapid expansion of anthropogenic activities that has occurred in the last decades. Landscape metrics are commonly used to define landscape patterns and to evaluate fragmentation processes. This investigation focuses on the performance of a set of landscape pattern indices within landscapes characterized by coastal environments and extent below 1,000 ha. The aim is to assess the degree of habitat fragmentation for the monitoring of protected areas and to learn whether values of landscape metrics can characterize fine-resolution landscape patterns. The study areas are three coastal wetlands belonging to the Natura 2000 network and sited on the Adriatic side of Apulia (Southern Italy). The Habitat Maps were derived from the Vegetation Maps generated integrating phytosociological relevés and Earth Observation data. In the three sites, a total of 16 habitat types were detected. A selected set of landscape metrics was applied in order to investigate their performance in assessing fragmentation and spatial patterns of habitats. The final results showed that the most significant landscape patterns are related to highly specialized habitat types closely linked to coastal environments. In interpreting the landscape patterns of these highly specialized habitats, some specific ecological factors were taken into account. The shape indices were the most useful in assessing the degree of fragmentation of habitat types that usually have elongated morphology along the shoreline or the coastal lagoons. In all the cases, to be meaningful, data obtained from the application of the selected indices were jointly assessed, especially at the class level.