Aim: The Aegean Sea constitutes a major biogeographic barrier between the European and Asian continents and several models of diversification in the Aegean have been documented. Here we test three of those models for the Aegean green-lizards (Lacerta trilineata–pamphylica group): Vicariance vs. Overland Dispersal vs. Island Stepping-stone Dispersal. We investigate these hypotheses and complement our knowledge on the impact of the Aegean Barrier on east Mediterranean taxa. Location: Aegean Sea, east Mediterranean Taxon: Lacerta lizards Methods: We analysed ddRAD loci (double-digest restriction-site-associated DNA) to estimate species-trees under coalescent models and maximum likelihood trees using concatenation. We performed hierarchical population structure analyses and inferred ancestral distribution-areas. We also sequenced the complete cytochrome b gene and produced a time-calibrated mtDNA gene-tree tree to conduct a critical comparison with previous studies. Results: Aegean green-lizards diverged into four main groups in parallel during the Late Pliocene with distributions to the East and West of the Aegean. The Eastern group includes Lacerta pamphylica and East Aegean L. trilineata, while the Western group contains the Central Cyclades populations and the remaining populations of the Balkan Peninsula. The Aegean green-lizards’ ancestor occurred in Anatolia, while the West lineage ancestor occurred in the Central Cyclades islands, revealing a dispersal between the two regions. The radiations of all major green-lizard groups, including trilineata+pamphylica, occurred in parallel in the Late Pliocene. Main Conclusions: In contrast to previously suggested biogeographical hypotheses for the group, based on mtDNA, the Island Stepping-stone Dispersal scenario is strongly supported. Green lizards offer a rare paradigm of diversification in the Aegean, where populations largely expanded their geographical distribution and crossed the Aegean Barrier by using the central Aegean islands as stepping stones.