The systematic research of amphipod genus NiphargusSchiødte, 1849 in Iran has begun only recently, and new field explorations result in discovery of new, yet undescribed species. Here we report on faunistic surveys in the Boyer-Ahmad Region that unveiled three species. Using molecular phylogeny (COI and 28S markers) and morphological analysis, we show that one species should be classified as the recently described N. persicus Esmaeili-Rineh, Sari, Fišer & Bargrizaneh, 2017, whereas the other two are new to Science. We show that both species, N. yasujensis n. sp. and N. nasrullahi n. sp., fall into the Middle East clade of species, as well as that both species are genetically and morphologically distinct from other species in the region. Both species are diagnosed, described and illustrated.