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Lacerta pamphylica and Lacerta trilineata are two currently recognized green lizard species with a historically problematic taxonomy. In cases of tangled phylogenies, next‐generation sequencing and double‐digest restriction‐site‐associated DNA protocols can provide a wealth of genomic data and resolve difficult taxonomic issues. Here, we generated genome‐wide SNPs and mitochondrial sequences, and applied molecular species delimitation approaches to provide a stable taxonomy for the Aegean green lizards. Mitochondrial gene trees, genetic cluster delimitation and population structure analyses converged into recognizing the populations of (a) L. pamphylica, (b) east Aegean islands, Anatolia and Thrace (diplochondrodes lineage), (c) central Aegean islands (citrovittata), and (d) remaining Balkan populations and islands (trilineata), as separate clusters. Phylogenomic analyses revealed a split into two major clades, east and west of the Aegean Barrier, unambiguously showing a sister–clade relationship between pamphylica and diplochondrodes, rendering L. trilineata paraphyletic. Species delimitation models were tested in a Bayesian framework using the genomic SNPs: lumping all populations into a single ‘species’ had the lowest likelihood but the current taxonomy was also outperformed by all other models. All lines of evidence support the Pamphylian green lizard as a valid species; thus, east Aegean L. trilineata should also be considered a distinct species under the name Lacerta diplochondrodes. Finally, evidence from the mitochondrial and nuclear genomes is overwhelmingly in favour of recognizing the morphologically distinct Cycladian green lizards as a distinct species. We propose their elevation to full species under the name Lacerta citrovittata. All remaining insular and continental populations of the Balkan Peninsula represent the species L. trilineata.

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1. A revision of Anatolian L. trilineata reveals its subdivision into three species: The western L. trilineata BEDRIAGA, 1886 (comprising in Anatolia the two subspecies- groupings cariensis and diplochondrodes), the eastern L. media LANTZ & CYREN, 1920 (comprising the subspecies L. m. (m.) media - probably subdivided into further „minor subspecies` - L. m. (i.) isaurica, L. m. (i.) ciliciensis, L. m. (w.) wolterstorffi, L. m. (w.) israelica) and L. pamphylica SCHMIDTLER, 1975; the latter being endemic and allopatric in Southern Central Anatolia. Probably these three species are equally related with each other, with the L. viridis-strigata-complex and possibly also with L. agilis. In Green Lizards generally the degree of specific differentiation is weil indicated by the degree of pholidotic differentiation. 2. In the intrapontic transversal valleys of Arav and Gök-rivers (West Pontus-Subregion) three species of Green Lizards prove to be ecological indicator-species of the three main vegetation-zones and herpetocoenoses: - Mediterranean-intrapontic vegetation-zone (Pinus halepensis; 300-600 m): L. m. me- dia and the reptiles Ophisops elegans, Coluber caspius, Mauremys caspica, Testudo graeca; the amphibians Bufo viridis, Hyla arborea, Rana ridibunda. - Supramediterranean-prepontic vegetation-zone (Pinus nigra; 600-1000 m): L. triline- ata galatiensis and the reptiles Lacerta parva, Podarcis muralis, Emys orbicularis, Testudo graeca and, additionally to the above mentioned amphibians: Rana macrocnemis. - Moderate-euxinic vegetation-zone (Pinus silvestris; 1000-1500 m): L. viridis paphla- gonica and the reptiles Lacerta cf. rudis, Podarcis muralis, Coronella austriaca; the amphibi- ans Triturus vittatus, Bufo bufo, Hyla arborea, Rana ridibunda and R. macrocnemis.