Research into gene flow across interspecies hybrid zones gives an opportunity to identify mechanisms involved in the formation and maintenance of a species. The section of the hybrid zone between Microtus arvalis and M. obscurus in the Lower Oka basin (East European plain, Russia) was analysed here. Clinal analysis of nuclear and mitochondrial DNA and karyotypic and phenotypic features revealed a cline for mitochondrial gene Cytb; this cline exceeded in width clines for nuclear gene Tp53, for male-specific gene SMCY and for chromosomal markers. The phenotypic cline is second in width after the Cytb cline. The centre of the Cytb cline was found to be shifted from centres of the other clines towards the M. obscurus geographic range. Centres of the nuclear and chromosomal clines nearly coincide. The width of the Cytb cline and the shift of its centre can be explained by expansion of M. obscurus males into the geographic range of M. arvalis. The wide phenotypic cline may be caused by a large number of loci of small effect that determine the phenotypic features. Despite the expected negative correlation between the level of genetic divergence of the contacting forms and the width of the hybrid zones between them, the M. arvalis x M. obscurus hybrid zone in the studied section is wider when compared with the hybrid zones between phylogenetic lineages of M. arvalis in Southwest and Central Europe. We suppose that this discrepancy results from an influence of specific landscape features on the parameters of the hybrid zones. An inversion in autosome No. 5, which is an exclusive feature of M. obscurus, was absent to the west of the centre of the hybrid zone. The limited distribution of this inversion is suggestive of incompatibility of this chromosomal rearrangement with some genes of M. arvalis.