Abstract Historical biogeography and comparative phylogeography have much in common. Both seek to discover common historical patterns in the elements of biotas, although typically at different tiers of evolutionary history. Comparative phylogeography is based on phylogeographic analyses of multiple taxa, usually widespread species. By comparing the phylogeographic structures of numerous widespread sympatric species, one can infer whether the current fauna has been historically stable, as evidenced by the relative frequency of geographically congruent reciprocally monophyletic groups. Alternatively, if species distributions are ephemeral over evolutionary time, a mixture of phylogeographic structures is expected. Coalescence analyses contribute information about history irrespective of whether haplotype phylogenies are structured or not. In the aridlands of North America, several isolating events are evident in the phylogeographic patterns of birds, mammals and herps. A mid-peninsular seaway in Baja California, dated at ca. one million years before present, had a pervasive effect, with 13 of 16 assayed species showing a concordant split. Hence, this community appears to have been a stable assemblage of species over the past one million years. In contrast, the avifauna of the Sonoran-Chihuahuan deserts consists of two species with a concordant split and three other species that are undifferentiated across both deserts. Hence, the species in this area have had different histories. The Baja biota appears to resemble its ancestral configuration to a greater degree than the Sonoran-Chihuahuan one. A deeper evolutionary event separated taxa in Baja California from the eastern deserts, showing that the aridlands fauna was affected by events at different times resulting in overlain tiers of history.