The North-Western Mediterranean basin is well known for its high number of relictual endemic taxa, and has been indicated as one of the world’s major biodiversity hotspots at the species level. A possible contributing factor may be long-term persistence of populations and their prolonged stability. This study was designed to investigate the phylogeographic structure of three common species of the genus Lepidocyrtus (Hexapoda: Collembola), soil-dwelling arthropods characterized by limited dispersal capabilities and generally associated with forest habitats. We observed a remarkable geographic structure, with numerous deeply divergent genetic lineages occupying islands as well as mainland sites with no apparent gene flow among most sites, even across distances of only tens of kilometres. The reconstructed time frame for the evolution of these lineages suggests divergence between 5 and 15 Ma. This indicates a remarkably ancient origin and long-term persistence of individual lineages over a fine geographic scale despite the occurrence of abrupt sea level and climatic fluctuations in the area. This further suggests that currently recognized morphological species might be a serious underestimation of the true springtail biodiversity within this region.