Populations experiencing varying levels of ionising radiation provide an excellent opportunity to study the fundamental drivers of evolution. Radiation can cause mutations, and thus supply genetic variation; it can also select against individuals that are unable to cope with the physiological stresses associated with radiation exposure. Since the nuclear power plant explosion in 1986, the Chernobyl area has experienced a spatially heterogeneous exposure to varying levels of ionising radiation. We sampled Daphnia pulex (a freshwater crustacean) from lakes across the Chernobyl area, genotyped them at eleven microsatellite loci, and also calculated the current radiation dose rates. We then investigated whether the pattern of genetic diversity was shaped primarily by radiation-mediated supply of variation consistent with increased supply of de novo mutations, or by greater radiation-mediated selection at higher dose rates. We found that measures of genetic diversity, including expected heterozygosity (an unbiased indicator of diversity) were significantly higher in lakes that experienced higher radiation dose rates; this is consistent with mutation outweighing selection as the key evolutionary force in populations experiencing high radiation dose rates. We also found significant but weak population structure, and clear evidence for isolation by distance between populations. This evidence suggests that gene flow between nearby populations is eroding population structure, and that mutational input in high radiation lakes could, ultimately, supply genetic variation to lower radiation sites.