Niphargus fongi sp. n. (Amphipoda, Niphargidae) is described from a cave in the Dinaric karst of southeastern Slovenia and its morphology is reported in detail. Its occurrence in pools of percolating water, some of which temporarily dry up, and its narrow distribution range suggest that the species lives in limestone fissures, possibly in the epikarst ecotone. Small though distinct diagnostic morphological characters support the species hypothesis based on molecular evidence. Re-evaluation of the degree of morphological differentiation in the light of molecular findings implies that the term "cryptic species", at least in some less well-studied taxa, may also depend on taxonomic evaluation of morphologically distinct populations. Additionally, a species described from a poorly sampled habitat constitutes a sample case of where taxonomic as well as ecological influences on biodiversity become apparent. Both incomplete taxonomy as well as insufficient sampling affect estimates of biodiversity in subterranean habitats.