The biodiversity of transitional zones is unique, due to mixing and co-occurrence of biotic elements. Despite this, our basic knowledge on distributional patterns of soil microarthropods in areas where biogeographic regions overlap is insufficient. We studied the biogeographic patterns of Protura across three natural landforms in Ukraine within the Transcarpathia (Transcarpathian Lowland, Transcarpathian foothills, and Volcanic Ukrainian Carpathian), which are influenced by adjacent biogeographic areas (mainly Alpine and Pannonian). We hypothesised that these overlaps have brought about an increase in Protura diversity, due to inclusion of faunal elements from diverse origins and differing in geographical histories. Distinct differences in the species composition of Protura were found among lowland, foothill, and mountain sites within Transcarpathia. Mountain sites mainly have Protura species with a wide continental distribution, while species of the foothills mainly stem from the Pannonian biogeographic region. The highest number of proturan endemics was associated with the Transcarpathian foothills. We conclude that the Transcarpathian region can be defined as a biogeographical transition zone for soil microarthopods, exemplified by Protura, and that foothill sites such as the volcanic-tectonic mountain Chorna Hora is a local hotspot of diversity and endemism, representing the most valuable parts of Transcarpathia with respect to diversity and endemism.