The paper presents an overview of modern molecular genetic methods for identification of pathogenic bacteria. One of the main current methods is the polymerase chain reaction and its modifications. Agarose gel electrophoresis is used for PCR analysis. The authors presented the advantages of the real-time fluorescent tag on this stage (quantitative PCR, Quantitative PCR, Q-PCR, Real-Time PCR) and Flash PCR. Real-Time PCR permits quantitative analysis of a test sample and reduces analysis time. Simplified version of the PCR detection of the fluorescent signal is Flash PCR. In addition to PCR, there are other methods based on the amplification of DNA, in particular, the ligase chain reaction. Considered sophisticated methods of identification of pathogenic bacteria--multilocus sequence typing, the analysis of variable nucleotide tandem repeats. One of the most convenient methods for the complete identification of pathogenic bacteria can be sequenced bacterial genome.