Refugia featured prominently in shaping evolutionary trajectories during repeated cycles of glaciation in the Quaternary, particularly in the Northern Hemisphere. The Southern Hemisphere instead experienced cycles of severe aridification but little is known about the temporal presence and role of refugia for arid‐adapted biota. Isolated mountain ranges located in the Australian arid zone likely provided refugia for many species following Mio/Pliocene (Heteronotia that have distributions confined to major rocky ranges in the arid zone. Phylogenetic analyses show that each rocky range harbours a divergent lineage, and substantial intraspecific diversity is likely due to topographic complexity in these areas. Old divergences (∼4 Ma) among lineages pre‐date the formation of the geologically young sand deserts (