Connectivity between populations is a key factor that influences both their dynamics and the genetic structuring of marine species. In this study, we explored connectivity patterns of a long-dispersing species, the edible common sea urchin Paracentrotus lividus, focusing mainly on the Adriatic-Ionian basins. We applied a multidisciplinary approach integrating population genomics, based on 1122 Single Nucleotide Polymorphisms (SNPs) obtained by 2b-RAD in 275 samples, with Lagrangian simulations performed with a biophysical model of larval dispersal. We detected genetic homogeneity among eight population samples spanning about 600 km and collected in the focal area (Adriatic-Ionian basins), whereas weak but significant differentiation was found with respect to comparative samples taken from French and Tunisian coasts. Genetic analyses performed separately with putatively neutral and outlier loci confirmed genetic homogeneity within Adriatic-Ionian basins, but showed a much higher differentiation at the large scale. Lagrangian simulations found a significant potential for larval exchange among the eight Adriatic-Ionian locations, supporting the view of strong connectivity of P. lividus populations in this area. A peculiar pattern emerged from the comparison of our results with those obtained from published P. lividus cytochrome b (cytb) sequences, which revealed genetic differentiation in the same area despite a smaller sample size and a lower power to detect differences. Comparison with studies conducted in the same Adriatic-Ionian locations using nuclear markers on other species having similar pelagic larval durations highlights differences both in realized and potential connectivity patterns, and warns from generalizing single-species results to the entire community of rocky shore habitats.