The importance of hybridization in animal evolution has become controversial. Gene flow between divergent taxa can strongly influence processes of great interest to evolutionary biologists, such as speciation and adaptation. Mitochondrial DNA (mtDNA) introgression is a commonly observed, yet particularly poorly understood consequence of hybridization between divergent taxa. Several known cases of mtDNA introgression exist that are heterogeneous in time and space, and it is unknown whether this represents the influence of extrinsic factors, such as selection and demographic fluctuation, or more intrinsic ones, such as cytonuclear interactions or the mosaic evolution of reproductive isolation. It is usually assumed, on the basis of the apparent lack of hybrids at zones of contact, that this phenomenon is unaccompanied by further admixture at nuclear loci, although this assumption rarely is tested. We present an analysis of population structure and gene flow across a zone of mitochondrial introgression between 2 nonsister species of chipmunk (Sciuridae: Tamias). We examined patterns of variation in 11 nuclear markers (10 microsatellites and 1 sequence-based marker) and compared them with previously identified patterns of mtDNA variation. We found little evidence of nuclear gene flow but some correspondence of introgression with microsatellite population structure. This work suggests that a complex interaction of ecological and genetic factors could have structured introgression of mtDNA in this system.