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In this paper we present the seabed maps of the shallow-water areas of Lampedusa and Linosa, belonging to the Pelagie Islands Marine Protected Area. Two surveys were carried out ("Lampedusa 2015" and "Linosa 2016") to collect bathymetric and acoustic backscatter data through the use of a Reson SeaBat 7125 high-resolution multibeam system. Ground-truth data, in the form of grab samples and diver video-observations, were also collected during both surveys. Sediment samples were analyzed for grain size, while video images were analyzed and described revealing the acoustic seabed and other bio-physical characteristics. A map of seabed classification, including sediment types and seagrass distribution, was produced using the tool Remote Sensing Object Based Image Analysis (RSOBIA) by integrating information derived from backscatter data and bathy-morphological features, validated by ground-truth data. This allows to create a first seabed maps (i.e. benthoscape classification), of Lampedusa and Linosa, at scale 1:20 000 and 1:32 000, respectively, that will be checked and implemented through further surveys. The results point out a very rich and largely variable marine ecosystem on the seabed surrounding the two islands, with the occurrence of priority habitats, and will be of support for a more comprehensive maritime spatial planning of the Marine Protected Area. [ABSTRACT FROM AUTHOR]