The aim of the work was to conduct a comparative phylogenetic analysis based on wgSNP of complete genomes of Brucella melitensis strains circulating in the territory of the Russian Federation. Materials and methods . wgSNP typing of 412 B. melitensis strains of the main genetic lineages of brucella from different regions of the world, including 64 strains isolated in the regions of the European and Asian parts of the Russian Federation, was performed. DNA sequencing was conducted on the “Ion GeneStudio S5 Plus” platform (“Life Technologies”, USA) using the “Ion Plus Fragment Library Kit library preparation” (“Life Technologies”, USA), according to the “Ion 520™ & Ion 530™ Kit – Chef” protocol (Revision D.0). Results and discussion . It has been established that the strains circulating in Russia belong mainly to genotype II, which has a wide geographical distribution across the territory of Eurasia. At the same time, subgenotype IIh prevails in the regions of Siberia, and Iii – in the European territory of the country. For the first time, sets of specific SNPs have been identified that allow for intraspecific differentiation of B. melitensis strains. The obtained results made it possible to determine the probable routes of introduction of the causative agent of brucellosis into the territory of the Russian Federation from China and the countries of the Middle East. The prospect of using an optimized wgSNP typing scheme to solve urgent problems in the field of molecular epidemiology of brucellosis is demonstrated. It includes determining the genotype and subgenotype of the pathogen associated with the probable geographical region of origin of infection, and identifying the genetic relations between strains with high accuracy.