At radioactive sites, at least two mechanisms may affect the genetic diversity of populations of a given species. Increased mutation rates due to radiation exposure may increase the amount of genetic diversity in a population. Alternatively, population bottlenecks exacerbated by environmental degradation may lead to a reduction of diversity. The relationship between these two contradictory forces is complex. To explore this relationship, long-term monitoring of a genetic marker within a population is needed. To provide baseline data on the population genetics of the bank vole (Clethrionomys glareolus) living in the most contaminated regions at Chornobyl, Ukraine, we have sequenced 291 base pairs of the mitochondrial DNA control region. Bank voles were chosen as a model system because they have the highest levels of internal dose of cesium-134, cesium-137, and strontium-90 within the Chornobyl exclusion zone. We sampled three geographic sites, which were Oranoe, a reference site with virtually no radioactive contamination (<2 Ci/km2), and two highly contaminated sites, Glyboke Lake and the Red Forest (both 1,000 Ci/km2). Genetic diversity in the population from Red Forest (0.722 ± 0.024) was significantly greater than at the Oranoe reference site (0.615 ± 0.039), while genetic diversity at Glyboke Lake (0.677 ± 0.068) was intermediate. It is concluded that long-term studies of historical and demographic characteristics for experimental and reference populations are required in order to employ population genetics to understand the biological impact of environmental contaminants on the genetics of natural populations.