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As for today, nanodiamonds (NDs) are widely used in the different areas of science and industry. One of the actively developing sphere of the NDs applications is biomedicine: nanodiamonds can be used as fluorescent biomarkers, drug carriers, adsorbents, or as bases of various bioconjugates. One of the properties that define the effectiveness of NDs in biomedical applications is their fluorescence by which they can be visualized in the living organism. However, tissue molecules and different drugs attached to the NDs surface often have their own bright fluorescence. This background fluorescence impedes the qualitative visualization of nanodiamonds. One of the way to circumvent this obstacle is to understand and incorporate in the visualization technique the properties and mechanisms of the NDs’ ‘neighbor’ molecules fluorescence. In particular, it is known that different nanoparticles quench the fluorescence of bioactive molecules. The study of such quenching by nanodiamonds will provide the insight in the NDs’ visualization as well as the possible way to track the loading and subsequent unloading of drugs from the NDs’ surface. In this work the quenching of the fluorescence of two bioactive molecules – the enzyme protein Hen Egg White Lysozyme (Lys) and modern anticancer drug Doxorubicine (Dox) – by the detonation nanodiamonds of two different sizes – 5 nm and 10 nm – was studied by the methods of spectrofluorimetry. It was found that the fluorescence of both bioactive molecules is quenched by the NDs of both sizes. However, it was found that quenching mechanisms are different for two molecules: the quenching of Lys fluorescence is static, the quenching of Dox fluorescence is the combination of both static and dynamic mechanisms. Using the obtained results the Stern-Vollmer quenching constant of Lys by both sizes of NDs was calculated, the hypothesis on the difference of the quenching mechanisms of Lys and Dox fluorescence by NDs has been proposed.