Secondary contact zones have been formed between several pairs of avian species and subspecies in northern and northeastern Iran during the post-Pleistocene and Holocene times. Three subspecies groups out of the four in the great tit (Parus major), namely, major, bokharensis and cinereus are supposed to have come into local or regional secondary contact in northeastern Iran. Parus major intermedius known from this region, has long been suggested to have a hybrid origin, stemming from hybridization between the yellow western (major) subspecies group and the grey eastern (bokharensis or cinereus) subspecies group, based on intermediate plumage coloration. Here, we investigated the evidence of intergradation between subspecies groups and the evolutionary origin of P. m. intermedius using mitochondrial DNA sequences (236 individuals, control region) and microsatellites (73 individuals, 11 loci) and used Approximate Bayesian computation to test competing scenarios of demographic history of the studied populations. Our analyses indicate a divergence origin for intermedius, resulting from the expansion of major subspecies group. The low mitochondrial diversity (p = 0.00065, q = 0.00170) and high genetic differentiation in comparison with central populations suggest that intermedius is a peripheral population. Microsatellite results show no signs of nuclear admixture between bokharensis and major subspecies groups. However, one phenotypically intermedius specimen had bokharensis mtDNA and major nuclear DNA in the assumed hybrid zone (Lotf Abad), supporting past introgression.