Phylogeographic studies from western Palaearctic have generally focused on species able to disperse and track their emerging suitable habitats after the last ice age. However, data on species whose biogeographical histories differ from this bulk of Palaearctic fauna are scarce. This is clearly the case of some specialized organisms inhabiting inland hypersaline environments, which are likely to have had a wider distribution range during the late Tertiary and may have persisted through the Pleistocene to the present day only constituting relict populations. In this study, we use partial sequences from two mitochondrial genes [16S rRNA (16S) and cytochrome oxidase subunit II (COII)] to investigate the phylogeography of the Iberian populations of Mioscirtus wagneri (Orthoptera: Acrididae), a specialized grasshopper exclusively inhabiting hypersaline low grounds. Our results show that M. wagneri exhibits a marked phylogeographical structure, forming three main clades which correspond with populations located in north-east, central–south-east and south-west Iberia. These geographical areas did not share any haplotype, indicating that gene flow between them is absent. Nested clade analyses revealed that these lineages have probably evolved in allopatry and data on sequence divergence suggest population fragmentation from the Early Pleistocene. Overall, these results provide a broader perspective on the contribution of historical climate/geological events to biogeographical patterns of organisms currently forming relict populations of great conservation concern. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 623–633.