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Montane biodiversity is particularly vulnerable to rapid oscillations in environmental conditions. Recent modelling showed that only three of the 19 butterfly species of Erebia (Nymphalidae, Satyrinae) currently present in Iberia would persist in a worst‐case scenario for 2070. One of them is Erebia palarica, endemic to Northwest Spain. We combined genetics, morphometrics and ecological niche modelling to reconstruct its evolutionary history.First, sequences of the cytochrome oxidase I (COI) mitochondrial gene obtained from 305 specimens revealed a double star‐like network that suggests a demographic expansion from two ancestral populations. This finding is congruent with the larger and disjunct putative distribution revealed by climatic modelling during the Last Glacial Maximum.Second, genotyping of 262 samples with seven microsatellite markers produced a large cluster at the centre‐East of the Cantabrian range, mostly affected by isolation by distance, and revealed different levels of structure in the western localities.Lastly, we reviewed the intraspecific taxonomy of the species. The westernmost site (Queixa) stands as a clearly separated unit according to genetic and morphometric analyses, which further supports its vague former description as subspecies E. p. castroviejoi.Altogether, the case of E. palarica exemplifies the complexity that narrow endemics can show and highlights that understanding the evolutionary history of species is crucial for designing adequate conservation strategies. [ABSTRACT FROM AUTHOR]