The taxonomic status and phylogenetic relationships of the Deepwater Goby, Ponticola bathybius, an endemic species in the southern Caspian Sea, which were previously unknown, are examined here. Deepwater Goby samples were collected from three southern Caspian Sea localities (southwest, mid-south, and southeast), and phylogenetic analyses were conducted using mitochondrial cytochrome b (cyt b) and S7 nuclear gene sequences with maximum likelihood and Bayesian approaches. Additionally, the Deepwater Goby's population genetic structure and demographic history were evaluated for cyt b. Results were highly congruent, providing strong support for inclusion of the Deepwater Goby in the genus Neogobius (tribe: Neogobiini), from its previous placement in the genus Ponticola (tribe: Ponticolini). AMOVA analyses showed significant differences between western and eastern sampling localities (P < 0.05) of Deepwater Goby, with moderate F_ST (0.095) divergence. The haplotype network appeared star-like in formation, with no apparent genetic structure, indicating high connectivity and gene flow, and supporting a single continuous population. Since the Deepwater Goby exhibits low mobility after settlement, except for some migration between deeper and shallower waters, gene flow primarily occurs through spread of pre-settlement post-larvae via regional water currents. Mismatch distribution and neutrality tests both indicated that the Deepwater Goby likely underwent a recent demographic expansion in the southern Caspian Sea, estimated at ∼247 kya during the Pleistocene epoch, coinciding with similar expansions of other Caspian Sea taxa.