Brown algae Fucus vesiculosus Linnaeus, Fucus serratus Linnaeus, Ascophyllum nodosum (Linnaeus) Le Jolis and Saccharina latissima (Linnaeus) C.E. Lane, C. Mayes, Druehl & G.W. Saunders collected from natural substrates and from storm emissions in one of the ecotopes of the Kandalaksha Bay of the White Sea (66°31' N 33°11' E) were used for comparative assessment of the content of low-molecular metabolites of micromycetes beloning to the genera Fusarium Link, Alternaria Nees, Penicillium Link, Aspergillus P. Micheli ex Haller, Myrothecium Tode, Cladosporium Link and others. After drying, the samples were crushed in a laboratory mill, a mixture of acetonitrile and water was used for extraction in a volume ratio of 84:16 with a consumption rate 10 mL per 1 g specimen. Extracts after 10-fold dilution with the buffer solution were analyzed using a set of certified enzyme-linked immunosorbent assay systems (Russia). The lower limit of quantitative measurements corresponded to an 85% level of antibody binding. All analyzed compounds – T-2 toxin, diacetoxiscirpenol, deoxynivalenol, zearalenone, fumonisins, alternariol, ochratoxin A, citrinin, PR-toxin, mycophenolic acid, aflatoxin B1, sterigmatocystin, cyclopiazonic acid, emodin, roridin A and ergot alkaloids – were found in the fresh thalli of F. vesiculosus, F. serratus, and A. nodosum. In the samples from the emissions, the profile of mycotoxins has been significantly changed. In F. vesiculosus and F. serratus the content of mycotoxins decreased sharply and uniformly and, as a result, the incidence of detection reduced to 8% and 15%. In A. nodosum, alternariol, aflatoxin B1 and mycophenolic acid were revealed in 17% of samples near the limits of determination of methods, and the other components of the complex could not be found. The mycotoxins were absent in the fresh thalli of S. latissima, and only some of the samples from the emissions had weak contamination with mycophenolic acid and emodin.