For the first time, a molecular characterisation study was carried out on nematodes of the genus Parafilaroides parasitising the respiratory tract of Caspian (Pusa caspica) and Baikal (P. sibirica) seals. These seals live in isolation in the Caspian Sea and Lake Baikal respectively; water bodies which have no connection with the ocean. The lungworms were originally described as P. caspicus (Caspian seals) and P. krascheninnikovi (Baikal seals), but currently, do not have the status of valid species. The sequences of the D2-D3 of 28S and ITS2 rRNA gene and partial mitochondrial COI gene were obtained from the two forms of lungworms. The analysis of genetic distances showed that these two forms, despite their long-term isolation, are genetically close to each other and differ from P. gymnurus, which parasitises seals of the Phocinae living in seas of the northern hemisphere. Currently, P. krascheninnikovi is considered a synonym for P. gymnurus, but our initial findings dispute this statement. However, the clarification of taxonomic status of Parafilaroides parasitising the Caspian and Baikal seals needs further investigation using morphological methods and a larger sampling for the molecular analyses.