Nuclear genetic variation and population structure were assessed in 140 individuals from 16 populations across the range of the Danube crested newt (Triturus dobrogicus) using 40 enzyme loci. Intraspecific hybridization with other crested newt species (Triturus carnifex, T. cristatus, T. macedonicus and T. arntzeni) affected 33 individuals in 11 populations at the range edge and reduced operational sample size to 107 T. dobrogicus in 14 populations. Allele diversity was high, and we inferred a high level of gene flow among T. dobrogicus populations, possibly associated with flooding conditions and the relatively continous habitat along rivers. Triturus dobrogicus showed weak but significant genetic structure between tributaries of the three main river systems of Danube, Sava and Tisza. The highest genetic diversity was observed in the Sava drainage, suggesting that this area might have been a Pannonian refugium during the most recent glacial maximum. The relatively high level of genetic variation observed suggests that a genetic bottleneck during this period has not been extreme.