Aim We assessed genetic relationships among populations for each of the four snake species found on Crete (Zamenis situla, Hierophis gemonensis, Telescopus fallax and Natrix tessellata), including conspecific populations from the Aegean area. Our aim was to reconstruct their phylogeographical histories, especially regarding their occurrence on Crete. Location Crete, Aegean Sea and eastern Mediterranean. Methods Genetic diversity and relationships were based on sequences of the mitochondrial marker cytochrome b, applying phylogenetic analyses (maximum likelihood, Bayesian inference and neighbour-joining), a median-joining network analysis and a molecular dating analysis. Results The Z. situla phylogeny includes a clade with specimens from Crete, the Peloponnese and Thera, while specimens from Turkey, northern Greece and the eastern Aegean islands form a separate clade. The H. gemonensis tree also presents two clades: one comprising specimens from Crete and Kythera, and another representing the continental part of the species' distribution. For N. tessellata, Cretan populations are found as the sister clade to populations from Europe and western Turkey. A more complex genetic structure is found in T. fallax: specimens from Crete, Thera and Antikythera form a clade, which itself forms part of a western' clade, and an eastern' clade includes specimens from Turkey, the eastern Aegean islands and Cyprus. The splits resulting in the Cretan clades for T. fallax and N. tessellata occurred at the end of the Miocene and the Pliocene/Pleistocene boundary, respectively. The Cretan lineages of H. gemonensis and Z. situla diversified during the Pleistocene. Main conclusions Zamenis situla and H. gemonensis exhibit a phylogeographical pattern that involves a transmarine dispersal from southern continental Greece to Crete (possibly by humans in the case of Z. situla). The occurrence of T. fallax on Crete is explained by a natural dispersal from the west and isolation by vicariance. Although these two patterns have also been inferred for other studied herptiles of Crete, the pattern in N. tessellata is unique and involves a transmarine dispersal from south-western Turkey to Crete.