The Baikal 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 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 still 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 debated, and the placement of the Baikal and Caspian Seals 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 sequences 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, Nyakatura and Bininda-Emonds 2012).
Using a multigene mitochondrial dataset, Palo and Väinöla (2006) considered Pusa not to be a monophyletic group, with the Phocina forming a polytomy. Arnason et al. (2006), using whole mitochondrial genome sequences 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. Pusa caspica was suggested as basal to the Pusa genus, with Baikal and Ringed Seals as sister taxa. 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. The Baikal Seal is indicated as basal to the grouping of Pusa caspica and Halichoreus grypus, with a divergence time of around 1.6-2 million years ago. Nyakatura and Bininda-Emonds (2012) advocate subsuming Halichoreus and Pusa within the Phoca genus.