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The review presents the results of investigation of the interaction between the hydrophobic substrate hexadecane and microbial cells. Three aspects of this process are discussed in more detail: (1) interaction of bacterial cells with the hydrophobic substrate, including characteristics of the cell surface and the conformational changes occurring at contact between the cell and the insoluble substrate; (2) molecular basics of the degradation of hydrophobic compounds at each stage of the cell–substrate interaction, such as synthesis of dispersing components, dispersion of the water-insoluble substrate, sorption of the hydrophobic compound by the cell and its storage, as well as transcription regulation of the genes involved either directly in biodegradation or in the processes associated with growth on hydrophobic substrates; and (3) bacterial synthesis of surfactants in the course of the degradation of hydrophobic compounds, diversity of their structure and conditions for their enhance release, as well as their biotechnological application.