Cultivation of diatom algae is associated with many problems, one of which concerns the contamination of cultures with various microorganisms. A representative of kinetoplastids, the free-living bacteriotroph Bodo saltans Ehrenberg, 1832, can often be found among contaminants. In the case when B. saltans reaches a high abundance, diatom cells cease to divide, some of them die, becoming a substrate for the development of bacteria, and then the substrate for the next trophic link: kinetoplastids. For the decontamination of diatom cultures, we used amphotericin B, a polyene macrocyclic antibiotic active against some protozoa and fungi. The effect of the drug on B. saltans in cultures of eight species of diatoms, including Ardissonea crystallina (C. Agardh) Grunow, Climaconeis scalaris (Brebisson) E.J. Cox, Entomoneis paludosa (W. Smith) Reimer, Haslea karadagensis Davidovich, Gastineau & Mouget, Pleurosigma aestuarii (Brebisson ex Kutzing) W. Smith, Pleurosigma sp., Pseudo-nitzschia calliantha Lundholm, Moestrup & Hasle, and P. pungens (Grunow ex P.T. Cleve) Hasle, was investigated. The rate of division of diatom cells exposed to amphotericin B, depending on the dose and duration of exposure, was experimentally determined. Recommendations on the use of amphotericin B for the decontamination of diatom cultures from B. saltans are given.