Tatianaerhynchites aequatus (L.) (Coleoptera: Rhynchitidae), is an economically important pest species of fruit crops (Rosaceae). This study investigates population genetic structure of T. aequatus at the crossroads of biogeographic regions in Eastern Europe. To estimate gene flow and genetic variation, we sequenced a 794-bp fragment of the mitochondrial cytochrome oxidase I (cox1) gene in 52 specimens from 13 populations across the Republic of Moldova, Romania and Ukraine. Percent divergence among populations ranged from 0.09% to 2.14%. Nested clade analysis of 15 haplotypes showed evidence of genetic structuring that is inferred to be restricted gene flow/dispersal but with some long distance dispersal. Analysis of molecular variance showed genetic structuring and some level of restricted gene flow among populations. Haplotypes formation and distribution are related to biogeographic regionalization. We revealed that haplotype B is predominant, being the only one spread across all three biogeographic regions, indicating that this haplotype has a high adaptive potential. Knowledge on population structure and haplotypes with different adaptive potential may be important for pest management and biodiversity conservation programs.