Global climate changes during the Cenozoic (65.5 - 0 Ma) caused major biological range shifts and extinctions. In Northern Europe, for example, a pattern of few endemics and the dominance of wide-ranging species is thought to have been determined by the Pleistocene (2.59 – 0.01 Ma) glaciations. This study, in contrast, reveals an ancient subsurface fauna endemic to Britain and Ireland. Using a Bayesian phylogenetic approach we found that two species of stygobitic invertebrates (genus Niphargus) have not only survived the entire Pleistocene in refugia but have persisted for at least 19.5 million years. Other Niphargus species form distinct cryptic taxa that diverged from their nearest continental relative between 5.6 and 1.0 Ma. The study also reveals an unusual biogeographical pattern in the Niphargus genus. It originated in Northwest Europe ~88 Ma and underwent a gradual range expansion. Phylogenetic diversity and species age are highest in Northwest Europe suggesting resilience to extreme climate change, and strongly contrasting the patterns seen in surface fauna. However, species diversity is highest in Southeast Europe indicating that once the genus spread to these areas (~ 25 Ma), geomorphological and climatic conditions enabled much higher diversification. Our study highlights that groundwater ecosystems provide an important contribution to biodiversity and offer insight into the interactions between biological and climatic processes.