Sequencing of gene p66 fragments of 246-337 p.b. was performed in 45 isolates of Aorrelia afzelii isolated from different transmitting agents and reservoir hosts within the habitation area of the spirochaeta. At least seven allele variants of the pathogenic agent were found indifferent natural foci of the disease. The extent of similarity between the nucleotide sequences of the isolates of the same allele variant was 99.9-100%; the extent of similarity between different allele variants was 98.9-99.7%. It was found that the majority of genovariants of A. afzelii (with respect to 5S-23S) incorporated several different allele variants of gene p66, all allele variants being found in the two genogroups (VS461 and NT28) of the pathogenic agent.