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Detection and identification of microorganisms in aquatic environments is a challenging task for remote sensing. Fluorescence measurements of fungal particles (for example, mycelium and spores) could be very important for assessment of the presence of fungi in water sources, their biomass estimation and to study biodeterioration. Fungi can be detected in the laboratory and using remote sensing techniques (Raimondi et al., 2007). The aim of our study was to assess the opportunities of fluorescence spectroscopy as technique for microscopic fungi detection, classification of parts of fungal biomass (mycelium and spores), and discrimination between several fungal strains. The strains with different pigmentation Trichoderma harzianum, Alternaria alternatа and Cladosporium cladosporioides (kindly provided by Marfenina O.E. and Ivanova A.E., Soil Science Faculty of Moscow State University) were examined at various stages of their growth as suspensions in aquatic medium, as well as in presence of dissolved humic substances. Fluorescence emission spectra were measured using a luminescence spectrometer Solar CM2203 at several wavelengths of the exciting radiation (270, 310, 325 and 355 nm) for liquid samples placed in quartz cuvettes. The correlation between spores numbers and fluorescence intensities has been revealed. The fluorescence reflection spectra of mycelium and spores on agar nutrient media were detected using photometer Solar PB2201. Results demonstrate the feasibility of fluorescence measurements to detect fungal biomass in situ and in vivo and to discriminate between the examined strains in aquatic medium in presence of humic substances as background fluorophores. The research was supported by Russian Foundation of Basic Research (grant 16-34-00690 mol_a).