Crested newts (Triturus cristatus superspecies) are a group of closely related species with parapatric distributions that are likely to interbreed where their ranges meet. Coexistence of three species of the complex (Triturus cristatus, T. dobrogicus and T. carnifex) has been recently confirmed in central Europe. In this study we aim to elucidate the distribution of crested newts in contact zones in the Czech Republic and Slovakia, and determine the extent of hybridization and introgression using nuclear (microsatellites and Randomly Amplified Polymorphic DNA, RAPD) and mitochondrial DNA (mtDNA) markers. Nuclear markers reveal hybrid zones between T. cristatus and T. dobrogicus at the foothills of the Carpathians in southern Slovakia, and between T. cristatus and T. carnifex in the southern parts of the Czech Republic. Analysis of mitochondrial cytochrome b sequences reveals T. cristatus and T. dobrogicus-specific haplotypes in contact zones in southern Slovakia. Surprisingly, most T. carnifex and individuals with mixed ancestry between T. carnifex and T. cristatus possess haplotypes specific for T. dobrogicus, most likely as a result of historical mtDNA introgression. Only one T. carnifex-specific haplotype carried by a single specimen is found in the Czech Republic. Our study shows that genetic structure of central European populations of crested newts is complex and influenced by historical and contemporary hybridization.