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The article discusses the complex digital transformation problem for the functioning aqua-biotechnological industrial company. The structure of the information model and digital twin for such objects is identified and described. The results of a comprehensive engineering and economic inspection of the state of the biotechnological, engineering, and economic system from the point of view of digital transformation are described. A conceptual scheme of the enterprise functioning based on the results of digital transformation is presented. The target effects of modernization and reconstruction of the existing biotechnological enterprise based on the end-to-end digital technologies of the fourth industrial revolution are formulated.