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The Palaearctic genus <i>Niphargus</i> is a promising model system to understand subterranean fauna genesis in Europe. The Pannonian Plain (mainly covered by Hungary) in Central Europe, once being the area of the Paratethys, is a key area for <i>Niphargus</i> diversification. However, our knowledge on Hungarian species of <i>Niphargus</i> is primarily based on sporadic taxonomical works from the pre-molecular era. Here, we studied 14 localities, covering the eight valid Hungarian species of <i>Niphargus</i> and including nine previously unstudied populations. Based on sequences of three gene fragments, we reconstructed their phylogeny using maximum likelihood and Bayesian approaches. We found that not all Hungarian species of <i>Niphargus</i> are closely related, and even species sampled at the same localities can belong to different clades. Some Hungarian species form monophyletic clades, while others are nested in various non-Hungarian lineages. The new populations are all genetically distinct from the known species. Our results suggest that the Hungarian <i>Niphargus</i> fauna has originated from seven unrelated clades and its diversity is underestimated due to unknown populations and cryptic species. The detection of genetically distinct species of <i>Niphargus</i> from non-carbonate regions calls for further research efforts. The high diversity and the number of putative new species in the <i>N. tatrensis</i> clade warrants further, high-resolution phylogenetic studies.