The work presented in this thesis is the result of a Ph.D. project conducted at the Lundbeck Foundation GeoGenetics Centre at the GLOBE Institute, Faculty of Health, University of Copenhagen (initially as a part of the Natural History Museum of Denmark). The project was supervised by Morten Erik Allentoft and co-supervised by Rasmus Nielsen and funded by the Independent Research Fund Denmark (Det Frie Forskningsråd, DFF). In this thesis, findings from one published- and three unpublished papers are presented. The thesis consists of an introductory Chapter 1, in the form of review in preparation for submission, of the scientific research history and the future genomic potential of the Bombina hybrid zone. Then follows an outline of the thesis objectives. Chapter 2 concerns the hybrid zone dynamics in the Mátra Mountains in Hungary, where previous and very limited results are revisited using an extensive full-exome dataset, created as part of this thesis. In this chapter, the hybrid zone structure is examined, by means of the metrics reviewed in the introduction as well as state-of-the-art population genomics methods. Chapter 3 concerns the use of a novel approach for examining the Bombina hybrid zone, namely by use of admixture mapping, combined with Bombina-specific phenotypic measures. In this chapter, all genes in the dataset are scanned for significant association to the phenotypes, thereby potentially uncovering genes involved in divergent belly-colours across the zone. Chapter 4 is a published paper, testing the genomic potential in old ethanol preserved museum specimens, with the motivation of defining an ancient DNA method that enables the use of the many Bombina samples stored in museums around the world for genomic research. Then follows a review of the of the main conclusions of the thesis, including a summary of the results from each chapter, and future perspectives.