The molecular systematics of the subterranean amphipod genus Haploginglymus is addressed through the phylogenetic analysis of three DNA gene fragments (nuclear ribosomal 28S and protein-coding Histone 3, plus mitochondrial Cytochrome c Oxidase subunit I). We take advantage of the description of a new species from southern Spain (Haploginglymus geos sp. nov.) to assess the singularity of this genus endemic to the Iberian Peninsula and the inclusion of the morphologically aberrant H. morenoi within Haploginglymus. Our results corroborate the monophyly of the family Niphargidae but shows Niphargus to be paraphyletic as it currently stands, with Haploginglymus appearing nested within it. A strongly supported sister-group relationship between niphargids and the (thalassoid) pseudoniphargids is recovered as well, but we propose the Niphargidae should continue to be considered as a primary limnic group for biogeographic purposes despite its presumed marine derivation. Our findings are in agreement with previous studies that suggest the family Niphargidae originated in the late Cretaceous in the NE Atlantic, from where it eventually expanded across continental Europe.