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Connectivity is a fundamental ecological property affecting stability, resilience and recovery of marine populations, in particular in networks of patchy habitats as the Mesophotic Biogenic Habitats of the Northern Adriatic Sea. Specific information on the dispersal behaviour of many species living in these habitats is lacking, thus the connectivity simulations were performed over different pelagic propagules duration and different reproductive seasons of six consecutive years, covering most of the possible dispersal behaviour variability. The connectivity simulations were analysed with graph analysis methods by characterizing each connectivity graph with several structural measures and by identifying sites with greatest individual and group centrality. We tested the hypothesis that geographic proximity of sites cannot be a proxy for the connectivity and that hydrodynamic connectivity is statistically significantly related to the observed beta diversity among the studied sites. Results showed that species with different pelagic propagules duration follow greatly different dispersal dynamics, and that the network of studied outcrops is only partially connected to coastal benthic populations. Our results also made possible a critical appraisal of the current conservation strategies, evidencing gaps in the existing network of protected Mesophotic Biogenic Habitats in the Northern Adriatic Sea. We suggest possible improvements for an efficient preservation strategy of these unique biodiversity hotspots by including a fundamental ecological process, the dispersal connectivity, into the process of decision making for conservation. • Hydrodynamic model simulations and graph analysis are useful for multispecies cross-scale connectivity studies. • Small and medium scale connectivity contributes to the heterogeneity of communities in networks of patchy habitats. • Different pelagic propagules duration and reproductive seasons determine different dispersal connectivity of species. • Dispersal among the North Adriatic Marine Biogenic Habitats and from surrounding coasts have independent dynamics. • More protected areas should be established to efficiently protect the dispersal connectivity among Marine Biogenic Habitats. [ABSTRACT FROM AUTHOR]