Aim To investigate factors that explain the spatial pattern of genetic diversity in three closely related species (Linaria glacialis, Linaria nevadensis and Chaenorhinum glareosum) endemic to a fragile high mountain ecosystem. Location The alpine belt of Sierra Nevada, Spain. Methods We analysed the spatial pattern of cpDNA diversity of the three species. To explain the distribution of genetic diversity, we investigated the effect of topographic features and the evolutionary history of the species (demography, habitat availability and colonization dynamics). Results Genetic diversity was heterogeneous across the landscape. We found moderate positive correlation values between genetic diversity indices of the two Linaria species. We also observed moderate negative correlation values between genetic diversity indices of C. glareosum and those of L. glacialis and L. nevadensis. Topographic variables correlated positively with genetic diversity of the Linaria species and negatively with genetic diversity of C. glareosum. Bayesian skyline plots (BSPs) displayed a shared demographic pattern with a population size stabilization/increase since the LGM (the last 21 kyr) in all three species. Discrete phylogeographical analyses showed similar patterns of westward diffusion for L. nevadensis and C. glareosum. Species distribution models pointed to similar range dynamics in all three species, with a reduction in range size since the LGM. Main conclusions Different dispersal abilities, demographic trends and colonization patterns can hardly explain the differences in spatial patterns of genetic diversity between the Linaria species and C. glareosum. In contrast, topographic features seem to be an important factor to explain the distribution of genetic diversity in the alpine belt of Sierra Nevada. We point to a relevant role of microniche partitioning in determining patterns of genetic diversity distribution in alpine Mediterranean ecosystems. Furthermore, we highlight the role of microhabitat heterogeneity in the maintenance of distinct lineages, species and genetic diversity in high mountain biodiversity hotspots.