Biobanking of patient- isolated microbial strains is a critically important tool for modern biomedical research, though it is associated with a complex of unresolved ethical and legal issues. The goal of this paper is to analyze the issues based on biobanking case studies at the National Medical Research Center of Coloproctology named after Ryzhykh AN. The focus is on the contradictions between the need for scientific progress and respect for the rights of donors, including obtaining informed consent and ensuring data confidentiality. The study material included legal documents and internal regulations describing how to work with microbial collections. During the analysis, isolated Russian legislation, lack of a clear legal status for biological samples and dependence of ethical aspects of work on local protocols and internal policy of the institution have been found out. The key conclusion is the urgent need to develop a specialized regulatory system that harmonizes the principles of bioethics with the practical tasks of biobanking, establishing clear rules for handling a patient’s microbiota and consent management mechanisms.