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Aim: Groundwater harbours an exceptional fauna and provides invaluable ecosystem services, yet is among the least explored and consequently least protected ecosystems. Successful protection of its biodiversity depends on complete species inventories, knowledge of species spatial distribution, and quantification of biodiversity patterns, as well as disentanglement of the processes that shaped biodiversity patterns. We studied the hyper‐speciose amphipod genus Niphargus as a model system within a global subterranean biodiversity hotspot. We linked the biodiversity patterns with possible underlying processes and discuss the needs to include information on different origins of biodiversity into conservation approaches. Location: Europe, Western Balkans. Methods: We analysed biodiversity patterns of Niphargus using two biodiversity metrics, species richness and phylogenetic diversity, on a grid‐based approach. To account for high cryptic diversity, we replaced nominal species with taxonomic units identified in unilocus delimitations (MOTUs). We built a time‐calibrated multilocus phylogeny of 512 Niphargus MOTUs from within and outside the study area, and calculated Faith's phylogenetic diversity, standardized effect sizes of phylogenetic diversity, and residual of phylogenetic diversity regressed onto species richness. Results: Within the study area, we recognized 245 MOTUs, belonging to different Niphargus clades. Species richness is highest in a north‐western hotspot, although some species‐rich cells were detected also in the south‐east. High phylogenetic diversity coincides with high species richness in the north‐west, while in the south‐east it is lower than expected. Main conclusions: We have shown that species richness does not predictably correlate with phylogenetic diversity. This difference suggests that different processes have led to the formation of species‐rich areas in the Western Balkans: through a combination of dispersal and speciation in the north‐west, and local radiation in the south‐east, respectively. This calls for caution in conservation strategies relying solely on number of species and may change the view on conservation priorities within this region. [ABSTRACT FROM AUTHOR]