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The development of microorganisms on the surface of building materials, in pores or cracks, leads to the destruction or dissolution of this material. One of the most common and effective ways to protect building materials and structures from microbiologically influenced corrosion (MIC) is the use of biocidal drugs. The biocidal activity of a number of fluorinated derivatives of 1,3-diazines and 1,2,4-triazoles against Bacillus mucilaginosus cells has been studied. This bacterium is an active destroyer of silicates and aluminosilicates. The mineral-destroying role of this microorganism is associated with the synthesis of exopolysaccharides and acidic low-molecular-weight metabolites. It was found that in a series of 6-fluorinated of 2-amino- (I), 2-hydroxy- (II), 2-mercapto- (III) and 2-methylthio- (IV) pyrimidines, 2-methylthio- (IV) derivatives have the greatest biocidal effect, the suppression zones vary from 25 mm to 35.5 mm at the studied concentrations (0.6, 6 and 60% (vol.)). Samples of fluorinated of 5-mercapto-1,2,4-triazoles (V) also showed a good protective effect: the zone of growth inhibition of Bacillus mucilaginosus are in the interval from 20.5 mm to 27.5 mm. The greatest biocidal effect is inherent in perfluoroalkyl substituents of the following structure: C6F13 (a), CF(CF3)OC3F7 (c); CF(CF3)OCF2CF(CF3)OC3F7 (d); CF(CF3)[OCF2CF(CF3)]2OC3F7 (e). Their use as a protective coating, especially concrete, will ensure a longer safe operation.