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Mountain regions have long been important for maintaining populations and genetic diversity of wild species, especially those species that require large areas to sustain viable populations. We examined wolves (Canis lupus) in the Caucasus, Carpathian, and Dinaric–Balkan regions, expecting these persistent populations to contain high genetic diversity and an overlap of the major haplogroups detected in earlier broad-scale investigations. We analyzed 926 mitochondrial DNA control region sequences, including 533 new samples whose geographic distribution allowed us to reduce sampling gaps observed in previous broad-scale studies. We estimated genetic variability, population structure, and phylogeographic relationships to evaluate the diversity and connectivity of populations throughout the study regions. We detected haplogroups H1 and H2 that overlapped across the study regions. Haplogroup H1 can be divided into three subgroups: H1A and H1B that partially overlap throughout the study regions, and H1C that was found only in wolves from Armenia. Haplogroup H2 was largely confined to the Carpathian and Dinaric–Balkan regions. Our analyses of population structure partly concurred with the haplogroup distribution and produced four major genetic clusters. Our results demonstrated high genetic diversity within the study regions, supporting their role in maintaining intraspecific variability in wolves and other species that require large areas to sustain viable populations. The unique diversity and north–south structure observed within the Caucasus emphasize the need for further research and conservation efforts in this highly biodiverse region. Our findings highlight the role of broad-scale planning in conserving evolutionary processes in this and other transboundary areas. [ABSTRACT FROM AUTHOR]