Laboratory diagnostics of plague was carried out in compliance with valid operational guidelines and regulations. But its peculiarity consisted in the performance of diagnostic investigations secondary to antimicrobial therapy with application of preparations characterized by the expressed activity towards gram-negative microorganisms, including the agent of plague (ceftriaxone, ciprolet, and amikacin). The studies revealed that under antibiotic treatment during the early phase of infection the most effective method for the laboratory plague diagnostics was PCR. Based on the results of the assay it was possible to establish not only provisional, but also the final diagnosis in a patient. Obtained was genetic characteristics of the strains isolated from the patient and the marmot, withdrawn at the patient’s place, using techniques of molecular-genetic analysis, in particular PCR, multilocus VNTR, and multilocus and genome-wide sequencing. Thereupon the strains were attributed to antique biovar of the main subspecies of plague agent. In addition, close relation to Y. pestis of the main subspecies isolated in the same focus in 2012 and to the strains from Mongolian Altai and Tuvinian mountain focus was determined based on phylogenetic analysis of the isolates.