Mice belonging to the Mus musculus species complex from the north-eastern Iranian Plateau (Khorasan province) have been genetically characterised for allozymic variation, mitochondrial DNA and Y chromosome type and compared with samples from other geographic regions. The present study shows the existence of a transition zone between pure M. m. musculus in the North and animals related to M. m. castaneus in the South. The origin of this transition (primary or secondary contact) and the various biogeographic scenarios about its origin are discussed in the light of these new data sets. The possible role of the Harirud valley in the geographic connection between Central Asia and the Middle East is discussed.