Coastal deserts are geologically dynamic areas of the Earth, affected by historical changes in sea levels and in some cases also by fault-line tectonic activity. An example of such a dynamic area is the Chilean coastal desert of the Antofagasta and Atacama regions, which harbours many endemic species, such as the bothriurid scorpion species Brachistosternus paposo and Brachistosternus roigalsinai. In this work, we carry out phylogeographic and population genetic analyses on these scorpions, using two mitochondrial (COI and cyt b) and two nuclear (Actin 5C and wingless) markers to identify species and population structuring, and link these findings to the geological history of the area. The geographical feature separating the two species is identified as the Huasco River, and distinguishing morphological features for these scorpions are presented. Population genetic and phylogeographic outcomes reflect an unstable history across this region for B. paposo and B. roigalsinai, related to sea-level changes affecting coastal habitats, including nearby islands.