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Oceanographic processes play a key role in influencing the structure of the marine planktonic ecosystems. Taking advantage of the quasi-simultaneous collection of a large ichthyoplanktonic dataset in different regions of the Central Mediterranean Sea (Italian/Maltese, Tunisian and Libyan waters), this study aimed at the identification of the main environmental drivers that control the structure of the larval fish assemblages. Spatial distribution and taxa composition were related to physical forcings (geostrophic currents and wind stress) and environmental conditions (bottom depth, temperature, salinity, chlorophyll-a concentration). ANOSIM and SIMPER identified contribution of fish taxa to the average Bray-Curtis dissimilarity among regions. In Italian and Libyan waters, two assemblages (neritic and oceanic) were identified, while a mixed assemblage characterized only some stations. Two neritic and one oceanic assemblages were discriminated in Tunisian waters. Random Forest classification model highlighted the essential role of the bathymetry, while Lagrangian simulations evidenced the action of the hydrodynamics in mixing neritic and oceanic assemblages in the Italian/Maltese and partially in Libyan waters. These findings highlighted the importance of the multidisciplinary approach and shed light on the potential value of the ichthyoplanktonic surveys for the assessment of the state of the marine ecosystem and the conservation of the fishery resources. [ABSTRACT FROM AUTHOR]