The Caspian Seal belongs to the Phocina group of northern seals, which includes the Ringed Seals (Pusa), the Harbour and Spotted Seals (Phoca), and the Grey Seal (Halichoerus). The radiation of the Phocina group is now believed to have started in the northern seas of the late Pliocene, 2-3 million years ago, and was accompanied by invasion of the continental basins, though the paleogeography in this period is not clear (Palo and Väinöla 2006, Fulton and Strobeck 2010).
The taxonomic relationships between the seals of the continental lakes and open ocean has long been contentious, and the placement of the Caspian Seal has varied between the genera Pusa and Phoca. Cladistic and phylogenetic studies from the 1970s to present based on morphology, and more recently mitochondrial and nuclear gene DNA sequence datasets, considered Phoca, Pusa, Histriophoca, and Pagophilus to be a monophyletic group (Wozencraft 2005). These analyses support two clades, Pagophilus and Histriophoca and the Phocina group, Phoca, Pusa, and Halichoerus (Rice 1998, Bininda-Emonds et al. 2007, Arnason et al. 2006, Fulton and Strobeck 2010, Nakatuya and Bininda-Emonds 2012) but the placement of Halichoreus within the group has been problematic.
Using a multigene mitochondrial dataset, Palo and Väinöla (2006) considered Pusa not to be a monophyletic group, with the Phocina forming a polytomy, but suggested that the Caspian Seal was most closely related to Halichoerus. Similarly, Arnason et al. (2006), using whole mitochondrial genome sequences also concluded the Caspian Seal to be most closely related to the Grey Seal, with the Baikal Seal forming a sister taxon, with Phoca and Ringed Seals outside this group. Fulton and Strobeck (2010) using nearly 9,000 base pairs of nuclear gene sequences and complete mtDNA genomes, placed Halichoreus basal to the group, with Pusa and Phoca as sister clades, and Pusa caspica basal to the Pusa genus. The most recent assessment (Nyakatura and Bininda-Emonds 2012), a super tree analysis of all carnivora combining 114 trees from the literature and 45,000 base pairs of DNA sequence, supports the grouping of Halichoreus within Pusa, with Phoca as a sister clade. Pusa caspica and Halichoreus grypus are indicated as sister species, diverging about 1.6 million years ago. Nyakatura and Bininda-Emonds (2012) advocate subsuming Halichoreus and Pusa within the Phoca genus.