Tortoises of the Testudo graeca complex inhabit a patchy range that covers part of three continents (Africa, Europe, Asia). It extends approximately 6500 km in an east-west direction from eastern Iran to the Moroccan Atlantic coast and about 1600 km in a north-south direction from the Danube Delta to the Libyan Cyrenaica Peninsula. Recent years have seen a rapid increase of recognized taxa. Based on morphological investigations, it was suggested that this group consists of as many as 20 distinct species and is paraphyletic with respect to T. kleinmanni sensu lato and T. marginata. Based on samples from representative localities of the entire range, we sequenced the mitochondrial cytochrome b gene and conducted nuclear genomic fingerprinting with ISSR PCR. The T. graeca complex is monophyletic and sister to a taxon consisting of T. kleinmanni sensu lato and T. marginata. The T. graeca complex comprises six well-supported mtDNA clades (A-F). Highest diversity is found in the Caucasian Region, where four clades occur in close neighbourhood. This suggests, in agreement with the fossil record, the Caucasian Region as a radiation centre. Clade A corresponds to haplotypes from the East Caucasus. It is the sister group of another clade (B) from North Africa and western Mediterranean islands. Clade C includes haplotypes from western Asia Minor, the southeastern Balkans and the western and central Caucasus Region. Its sister group is a fourth, widely distributed clade (D) from southern and eastern Asia Minor and the Levantine Region (Near East). Two further clades are distributed in Iran (E, northwestern and central Iran; F, eastern Iran). Distinctness of these six clades and sister group relationships of (A + B) and (C + D) are well-supported; however, the phylogeny of the resulting four clades (A + B), (C + D), E and F is poorly resolved. While in a previous study (Fritz et al., 2005a) all traditionally recognized Testudo species were highly distinct using mtDNA sequences and ISSR fingerprints, we detected within the T. graeca complex no nuclear genomic differentiation paralleling mtDNA clades. We conclude that all studied populations of the T. graeca complex are conspecific under the Biological Species Concept. There is major incongruence between mtDNA clades and morphologically defined taxa. Morphologically well-defined taxa, like T. g. armeniaca or T. g. floweri, nest within clades comprising also geographically neighbouring, but morphologically distinctive populations of other taxa (clade A: T. g. armeniaca, T. g. ibera, T. g. pallasi ; clade D: T. g. anamurensis, T. g. antakyensis, T. g. floweri, T. g. ibera, T. g. terrestris), while sequences of morphologically similar tortoises of the same subspecies (T. g. ibera sensu stricto or T. g. ibera sensu lato) scatter over two or three genetically distinct clades (A, C or A, C, D, respectively). This implies that pronounced morphological plasticity, resulting in phenotypes shaped by environmental pressure, masks genetic differentiation. To achieve a more realistic taxonomic arrangement reflecting mtDNA clades, we propose reducing the number of T. graeca subspecies considerably and regard in the eastern part of the range five subspecies as valid (T. g. armeniaca, T. g. buxtoni, T. g. ibera, T. g. terrestris, T. g. zarudnyi). As not all North African taxa were included in the present study, we refrain from synonymizing North African taxa with T. g. graeca (mtDNA clade B) that represents a further valid subspecies.