In temperate regions of the Earth Pleistocene, climatic fluctuations significantly influenced distribution of species. However, little is known on how glacial and interglacial cycles affected range dynamics of the species occupying lower latitudes. In this study, we investigated mitochondrial DNA (mtDNA) variation and reconstructed the potential current and past (during the mid‐Holocene, 6 ka BP, and the Last Glacial Maximum, LGM, 21 ka BP) distribution of Neurergus derjugini, an endangered amphibian species endemic to the mid‐Zagros Mountains in Iran and Iraq. Six haplotypes identified in the control region (D‐loop) form a well‐supported monophyletic clade, distinct from other Neurergus species and revealing a sister relationship to Neurergus kaiseri. Nucleotide diversity quantifying mean divergence between the sequences is low and does not support the recognition of distinct evolutionary lineages in Neurergus derjugini. The landscape connectivity analysis and the haplotype parsimony network reveal higher gene flow rate between the breeding streams in the southern part of the range, while the northern populations are more isolated. The potential distribution of Neurergus derjugini is restricted to valleys close to mountain tops, wherein very high elevations and dry habitats appear to be unsuitable. During the mid‐Holocene and LGM conditions, the range of the species may have been more extended and shifted to lower elevations. These findings show retraction of the Neurergus derjugini range during the Quaternary and indicate that range dynamics of the species occupying lower latitudes may not follow a scenario of glacial retraction and postglacial expansion.