Aim To assess spatial patterns of genetic and species-level diversity for Namib Desert Collembola using mitochondrial DNA cytochrome c oxidase subunit I (COI) gene sequences. Location Namib Desert gravel plains Taxon Collembola (springtails) Methods A total of 77 soil samples was collected along a NE-SW (60 km) and E-W (160 km) transects from within a 4000 km2 area of the Namib Desert gravel plains. We extracted 434 springtails from the 37 samples which contained Collembola and sequenced them at the COI gene locus. In the absence of previous genetic data for these taxa, we used GMYC analyses to provide putative species-level designations. Results We obtained 341 successful COI sequences, 175 of which were unique haplotypes. GMYC analyses identified 30 putative species, with up to 28% sequence divergence (uncorrected p-distance). The distribution of genetic variants was disjunct, with 97% of haplotypes and 70% of ‘GMYC species’ found only at single sites. Main conclusions Dispersal events, although rare, may be facilitated by environmental events such as prevailing onshore winds or occasional flow of rain water to the coast. We conclude that the high genetic diversity we observed is the result of ancient springtail lineages, patchy distribution of suitable habitats and limited dispersal/gene flow among habitable locations.