Assessing the effect of larval dispersal on the structures and dynamics of marine populations is still challenging. Connectivity has also crucial implications for the design of reserves and the evaluation of exploited stocks. The Lagrangian Flow Network methodology provides a full characterization of multiscale dispersal and connectivity for the dispersive stages of marine organisms, offering new opportunities in population genetics, fisheries and conservation biology. We subdivide the basin into sub-regions which are interconnected through the transport of larvae by ocean currents. The identification of hydrodynamical provinces and the computation of proxies measuring the retention and exchanges of larvae allow us to better understand how dispersion structure genetically marine populations and the relative role of larval dispersal and local adaptation to the environment on genetic differentiation. Another project explores the sensitivity of management units’ boundaries to connectivity processes. Focusing on Hake, we study the links between the mainland spawning areas and the recruited stock surrounding the Balearic Islands. Numerical experiments and long-term observations are combined to test if connectivity explains inter-annual variations of recruitment. Last, this methodology shows great promise as future developments (e.g. implementing habitat patchiness and the abiotic controls of larval production and survival) are handily accessible.