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Understanding how to relate the nanometer-scale phenomena and properties of source rocks and to their complex macroscopic properties is one of the current challenges in rock physics. This study shows a combined application of SEM, CLSM imaging and nanoindentation characterization, which provides the microscopic basis to analyze these macroscopically complex and heterogeneous rock samples. Organic matter was successfully imaged within the matrix of the Bazhenov Formation despite inherent lithologic differences of the phases. Nanoindentation measurements showed kerogen within the Bazhenov Formation to be softer than the surrounding mineral matrix. In particular, the Young’s modulus of kerogen from the Bazhenov Formation varies between 10 and 15 GPa, whereas bulk and shear moduli vary from 5 to 10 GPa and from 4 to 5 GPa, respectively. At different Poisson’s ratios, corresponding elastic properties measured and computed in this study and by others are in good agreement.