Niphargus Schiödte, 1849 is the most diverse subterranean amphipod genus in the West Palearctic, distributed between Ireland and Iran. The exploration of Niphargus diversity in the Zagros Mountains in Iran has begun a decade ago, and the number of newly described species is increasing fast. Recently, we collected several specimens of Niphargus from springs located in the northern parts of the Zagros Mountains in Iran. Detailed morphological observations and molecular phylogenetic analyses using 28S rDNA and COI markers revealed that these animals comprise two taxonomic units distinct from all hitherto described species. We hypothesize they should be treated as new species, named as Niphargus qalatianensis sp. nov. and Niphargus arasbaranensis sp. nov. Molecular phylogenetic analyses have shown that N. qalatianensis sp. nov. is nested within a monophyletic Middle Eastern clade known from previous studies. By contrast N. arasbaranensis sp. nov., is with low support associated to European species and suggests that the Iranian karst was not colonized two but three times. To gain a more comprehensive understanding of the intricate biogeographical history of the genus Niphargus in the Middle East, additional sampling in the region is imperative.