Monitoring of polar ecosystems is one of the most important areas of research in the use of Arctic territories in economic activities. An important place in such work is occupied by biomedical research aimed at identifying the risks of the occurrence of foci of infectious diseases in the areas of polar settlements.The purpose: to develop an algorithm for microbiological monitoring in the Arctic region.Materials and methods: classical bacteriological, mycological research, molecular-genetic,

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... I-TOF mass spectrometric analysis, phenotypic methods for determining antibiotic resistance, methods of mathematical data processing.Results and their discussion. The paper considers the scientific and methodological principles and the main stages of microbiota monitoring in the areas of polar settlements. The results of the study of samples from several territories along the Northern Sea Route are presented. The main habitats where potentially dangerous microorganisms should be detected are indicated. The role of anthropogenic invasion in the formation of Arctic microbiocenoses is noted. The trends of increasing the number and diversity of pathogenic microorganisms, both in the natural biocenoses of the Arctic and in the areas of polar settlements, are discussed. The necessity of microbiological monitoring as an integral part of epidemiological monitoring in the areas of Arctic settlements along the Northern Sea Route is substantiated.