© 2014 John Wiley & Sons Ltd. Aim: Granite outcrops may be able to act as refugia for species during adverse climate change, owing to their topographic complexity. We assessed this hypothesis by examining phylogeographical patterns in a common, geographically widespread granite endemic, Stypandra glauca (Hemerocallidaceae). Location: Granite outcrops of the Southwest Australian Floristic Region, Western Australia. Methods: Twenty-four tetraploid individuals of the granite endemic Stypandra glauca were sampled from each of 12 granite outcrops: 7 from a mesic environment and 5 from the semi-arid region. Phylogenetic reconstruction and divergence-dating was achieved using Bayesian and parsimony analyses of chloroplast haplotypes from 90 individuals. Nuclear diversity and population differentiation were analysed across all individuals using 10 microsatellite loci. Results: Stypandra glauca exhibited high (chloroplast) or moderate (nuclear) levels of divergence among, and low diversity within, outcrops. Haplotype diversity was high in both sampling regions, and each haplotype was unique to one outcrop. There was little correlation between geographical and genetic distance. Both nuclear and chloroplast diversity were higher in southern (mesic) outcrops than in northern (semi-arid) outcrops, although the level of chloroplast divergence among outcrops was similar for both climatic regions. Main conclusions: The levels of divergence and low diversity revealed in S. glauca support a scenario of prolonged isolation and persistence on granite outcrops in both mesic and semi-arid climatic regions, with no evidence of contraction-expansion dynamics across the outcrop network. The higher levels of diversity in the southern populations may result from the maintenance of a larger effective population size in southern regions, which retained more mesic climates during drier glacial periods. Although the climatic conditions differ between outcrops in this study, our results indicate that outcrops in both regions have harboured S. glauca throughout climatic changes, accentuating the value of these habitats to biodiversity conservation under future changing climate.