A new species of the genus Niphargus Schiödte, 1849 (Crustacea: Amphipoda: Niphargidae) is described from the deep pebble beach interstitial habitats along the northern Black Sea coastline, revealing a new type of environment for this amphipod genus and providing new insight into the diversity of this unusual biotope. Niphargus primoricussp. nov. belongs to “stygius–longicaudatus” species group corresponds to a distinct phylogenetic lineage, recently called “tarkhankuticus” ingroup (clade), which currently includes several species from the coastal areas of the Black Sea (Crimean Peninsula, southern Caucasus, and northern coast of the Republic of Türkiye [Turkey]). Molecular genetic analysis revealed that the speciation within this ingroup started in the Pliocene, approximately 5.76–3.6 Mya, and correlated with the Black Sea transgression. The divergence of the “tarkhankuticus” clade from the related European congeners probably occurred in the Late Miocene (~ 11–10 Mya), and is likely related to the separation of the Paratethys into different basins (Euxinian, Alpine and Pannonian). The new species has a wide distribution, currently inhabiting nearly 190 kilometers along the Black Sea coastline, from Gelendzhik to Khosta, and is characterized by a low level of genetic divergence between populations. The deep pebble interstitial coastal biotopes in the area are also inhabited by specific gammarid amphipods, for example, Dursogammarus dromaderus Marin & Palatov, 2022 and Litorogammarus dursi Marin, Palatov & Copilaş-Ciocianu, 2023 (Amphipoda: Gammaridae), whose biology has not been studied, and it is unknown how they spread along the coastline.