Mitochondrial and nuclear sequence data from two Antarctic ameronothroid mites, Halozetes belgicae and Alaskozetes antarcticus, were used to address three key questions important for understanding both the evolution of biodiversity and its future conservation in the Antarctic Peninsula Region: i) Do populations of mites across the Antarctic Peninsula and Scotia Arc constitute distinct genetic lineages? ii) What implications does the spatial genetic structure in these species have for current understanding of the region's glacial history? iii) What are the conservation implications of these findings? Our results indicate that both mite species have been present in the Antarctic since at least the Pliocene. At the regional scale, both species are comprised of a number of divergent, but sympatric, lineages that are genetically as distinct as some species within the genera Halozetes and Alaskozetes. At the local scale, complex structure suggests limited and stochastic post-Holocene dispersal. For both species, considerable spatial genetic structure exists across the region, similar to that found in other terrestrial invertebrates. These results support the implementation of stringent biosecurity measures for moving between the Scotia Arc islands and the Antarctic Peninsula, and throughout the latter, to conserve both evolutionary history and future evolutionary trajectories.