Due to their extraordinary coloration, mountain brook newts of the genus Neurergus found in the Near East have fascinated herpetologists since their initial description more than 150 years ago. Although the monophyly of Neurergus newts within the Salamandridae has been unambiguously shown for mitochondrial genes, and recent comprehensive molecular phylogenies placed Neurergus as a sister taxon of banded newts (genus Ommatotriton), we know almost nothing about the structure and relatedness of populations at the intraspecific level. In this study, we therefore analysed sequence variation of a mitochondrial DNA segment (covering a partial region of the control region and the 12S ribosomal RNA) from more than 100 individuals and of two nuclear genes (KIAA and SACS) for a representative subset of individuals originating from nine distinct populations, representing N. strauchii, N. crocatus and N. microspilotus. We also studied individuals of N. derjugini, a taxon that has long been synonymized as N. crocatus, and of which individuals have not been accessible to the scientific community since its original description in 1916. Our results suggest high genetic diversity of populations within species for the mitochondrial DNA marker, while the resolution of applied nuclear genes did not go beyond the level of species. For N. strauchii and N. crocatus, two species that inhabit the largest geographic ranges within the genus, we found a high proportion of diversity both within and between populations for the mitochondrial control region. Individuals of N. microspilotus and N. derjugini only displayed considerable genetic differentiation for one nuclear gene (SACS), while only very little or none genetic differentiation could be found for the mitochondrial control region and the KIAA gene, respectively. As both taxa are also morphologically not well differentiated, we suggest on the basis of the current dataset to taxonomically synonymize N. microspilotus due to priority reasons as N. derjugini. It can be therefore concluded that the most accurate taxonomy of the genus Neurergus should consider N. crocatus, N. strauchii, N. kaiseri and N. derjugini as valid taxonomic units at the species level.