The white wagtail (Motacilla alba) species complex with its distinctive plumage in separate geographical areas can serve as a model to test evolutionary hypotheses. Its extensive variety in plumage, despite the genetic similarity between taxa, and the evolutionary events connected to this variety are poorly understood. Therefore we sampled in the breeding range of the white wagtail: 338 individuals were analyzed from 74 areas in the Palearctic and Mediterranean. We studied the white wagtail complex based on two mitochondrial DNA markers to make inferences about the evolutionary history. Our phylogenetic trees highlight mtDNA sequences (ND2, CR), and one nuclear marker (CHD1Z), which partly correspond to earlier described clades: the northern Palearctic (clade N); eastern and central Asia (clade SE); southwestern Asia west to the British Isles (clade SW); and Morocco (clade M). The divergence of all clades occurred during the Pleistocene. We also used ecological niche modelling for three genetic lineages (excluding clade M); results showed congruence between niche and phylogenetic divergence in these clades. The results of the white wagtail ancestral area reconstruction showed the influence of dispersal on the distribution and divergence of this complex species. The most important vicariance event for the white wagtail complex may have been caused by the Gobi and Taklamakan deserts. We conclude that the ancestral area of the white wagtail complex was probably in the Mediterranean, with its geography having a considerable effect on speciation processes.