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Slow worms (Anguis spp.) are widely distributed in Europe. Based on pronounced divergences in molecular markers the subspecies of the slow worm, Anguis fragilis, have been recently elevated to species level. In Hungary both A. fragilis and A. colchica are present in the mountainous areas with their range being separated by the Danube River with potential contact zones in the Danube valley. Based on morphology, hybridization of the two taxa has been described earlier from the Budai and Pilis Mountains. In order to reveal the exact distribution and confirm hybridization of Anguis taxa in Hungary we analyzed fragments of mitochondrial (ND2) and nuclear (Rag1) genes in 36 specimens from eight regions of Hungary and adjacent countries. The results confirmed the previously known distribution pattern with an east-west split along the Danube River and supported the morphological findings about hybridization in the Budai and Pilis Mountains.