The article presents the results of the antimicrobial activity study of methanolic extracts obtained from previously unexplored six rare and endemic species (Alcea kusariensis, Cladochaeta candidissima, Sedum caucasicum, Iris reticulata, Platanus orientalis, Zelkova carpinifolia) of the Azerbaijani flora. The extracts were evaluated for their antimicrobial activity against strains of Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Staphylococcus aureus, Bacillus anthracoides and Candida albicans that are part of the normal human microflora and are considered opportunistic. This study has established that obtained both from whole plants and from different organs, both individually and in different combinations with each other, have sufficiently pronounced antimicrobial properties. Phytocoenosis of the growth sites of these species was also studied and described, and a corresponding GIS map was compiled.