Achromobacter spp. — opportunistic microorganism, causing nosocomial infections, which are especially dangerous for the patients from the departments of the reanimation and intensive therapy and pulmonology. This microorganism is very complicated in the identification by classical microbiological methods and by mass-spectrometry. The aim of this investigation was the development of the express-genotyping scheme with help of the molecular-genetic methods. This scheme allows to identify the species and the genotype of Achromobacter spp. on the base of the minimal targets number. The investigation was made on the biological samples from the patients, who were detected earlier in our research as infected by Achromobacter spp. Multi Locus Sequence Typing (MLST) was supplemented with targets important for the differential diagnostic and was used for research. The result of this work was the protocol of the Achromobacter spp. express-genotyping, which included the DNA isolation from the biological sample, amplification and sequencing of three genes: gltB, nrdA765 и bla-OXA, and following microorganism’s species and genotype detection. This protocol application allows to reduce the time and expenses for Achromobacter spp. identification and on the base of results to quarantine the patients, infected by the epidemiology important strains.