1. Cryptic species are an important part of freshwater biodiversity, yet it remains unclear how these species integrate into communities from local to regional geographic scales. To protect biodiversity, particularly overlooked cryptic species, an accurate understanding of the underlying processes and adequate level of protection is needed.
2. We analysed patterns of syntopies (local co-occurrences) and sympatries (regional range overlap) to explore how the phylogenetic origin of cryptic species shapes biodiversity patterns. We hypothesised (i) that syntopies were more common among distantly than closely related cryptic species, and (ii) that the existing sympatries were an outcome of phylogenetic relatedness and dispersal.
3. The hypotheses were tested on a polyphyletic species complex of subterranean amphipod species (Niphargus rhenorhodanensis complex) by deploying molecular species delimitation, time-calibrated phylogenies, and co-occurrence analyses with probabilistic and generalised linear models (GLM).
4. The studied complex comprised 37–48 molecular operational taxonomic units (MOTUs) from nine different clades, with syntopies occurring at random or less frequently than expected. GLM indicated age of divergence did not predict species sympatries, although they emerged more frequently among MOTUs from different clades. Sympatries, however, emerged through dispersal, in MOTUs with large geographic ranges. These mostly overlapped at the foothills of the Alps, the Jura and the Central Massif.
5. We conclude that the observed spatial patterns are mainly driven by dispersal and presumably reflect the geographic circumstances of speciation. While species richness on a local scale may be an outcome of competition and dispersal, regional biodiversity patterns presumably arise through a clade-level cascade of historical events, including orogeny and climatic shifts.