Aim The evolutionary history of narrow endemic species has received little attention compared with that of more widely distributed species. Small effective population sizes and long-term isolation of many narrow endemic species make research on their genetic make-up important for their future conservation. In this study we investigated the genetic variation and historical distribution of an isolated plant, the monospecific genus Pseudomisopates, as an example of the phylogeographical history of narrow endemics.Location Central Range, Iberian Peninsula, Mediterranean Europe.Methods We used amplified fragment length polymorphisms (AFLPs), nuclear and plastid DNA sequences and species distribution modelling. Sequence data were analysed using statistical parsimony, molecular dating, and a coalescent-based Bayesian model of isolation with migration. Genetic diversity and differentiation analyses based on AFLP data were performed. We compared the detection of clones using AFLPs with the results of a previous study that used simple sequence repeats (SSRs).Results AFLP analysis revealed that SSRs underestimate clone number. The coalescent-based Bayesian model of isolation with migration suggested a late Pleistocene divergence between the populations of Pseudomisopates on two mountain massifs (Gredos and La Serrota), despite the presence of a large area suitable for population admixture. Moderate to high levels of genetic diversity and high effective population sizes were inferred.Main conclusions Our results imply that the levels of genetic diversity within narrow endemic species from Mediterranean mountains could primarily be driven by extrinsic historical factors, rather than by intrinsic species-specific factors depending on their own biological characteristics. Narrow endemics are widely believed to harbour low genetic diversity because of small effective population sizes. However, this study and others on narrow endemic angiosperms demonstrate that narrow endemism does not necessarily result in low genetic diversity.