Bovine viral diarrhea is a widespread disease in the Russian Federation and causes significant economic damage to dairy cattle, especially under intensive commercial farming. The seropositivity of livestock in various Russian regions reaches 65-100 %. The disease is caused by two different virus species, BVDV-1 and BVDV-2, of which the latter is considered more virulent. The persistently infected (PI) animals which are a constant endogenous source of the virus in the herd play a major role in maintaining the stationary trouble of the farms. Short-term sources of the pathogen are transitively infected (TI) animals in which disease proceeds in acute form. Genetic structure of viruses circulating in local livestock populations gives necessary information about the evolution, geography and pathways of the pathogen. However, studies on the genetic polymorphism of viruses in Russia are not enough. This paper is the first to report on a phylogenetic analysis of two types of viral diarrhea virus, isolated from animals of foreign and domestic origin with different clinical manifestations of the disease. These data show the prevalence of BVDV-1b in PI and TI animals, as well as BVDV-2b and BVDV-2c circulation among Siberian dairy complexes (note, BVDV-2b and BVDV-2c in animals of foreign and domestic origin are detected in Russia for the first time). Phylogenetic analysis of viruses circulating among PI and TI of highly productive dairy cattle was based on a comparison of conserved region of viral genome (5´-UTR) using reverse transcriptase PCR (RT-PCR) method. Studies were conducted in five regions of Western and Eastern Siberia: Tyumen, Novosibirsk, Irkutsk regions, the Krasnoyarsk Territory and Northern Kazakhstan on big dairy farms with a population of 800 or more milking cows with an average annual productivity of 7,000-10,000 liters, where at the time of the research vaccination was not carried out or inactivated vaccines were used. The imported livestock was kept mainly in the Tyumen region and the Republic of Kazakhstan. Biomaterial (blood, serum, nasal discharge, lymphoid organs, lungs, vaginal discharges) was collected from clinically healthy persistently infected animals, transitively infected animals with reproductive disorders and respiratory syndrome, as well as aborted fetuses. A total of 479 samples were examined. According to our findings, two BVDV species circulate among the PI and TI animals on the big dairy farms. The phylogenetic analysis reveals seven subtypes of BVDV-1, i.e. 1a (5 %), 1b (35 %), 1c (5 %), 1d (10 %), 1f (20 %), 1i (5 %), 1p (5 %) and two subtypes of BVDV-2, i.e. 2b (10 %) and 2c (5 %). Taking into account the fact that the strategy of livestock breeding is changing in Russia, the number of dairy mega farms" is increasing, which receive animals with different infectious status from many sources. Thence, the study of the genetic polymorphism of the virus is topical. Comparison of data on the origin of animals with the results of phylogenetic analyses can help in determination of the sources and ways of bringing pathogens into a particular region and in identifying and tracking new and highly virulent strains of viruses. This is especially important during the implementation of vaccination programs for animals when the genetic profiles of vaccine strains do not coincide with the profiles of viruses circulating among animals in a particular area.