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Mechanobiology studies from the last decades have brought significant insights into many domains of biological research, from development to cellular signaling. However, mechano-regulation of subcellular components, especially membranous organelles, are only beginning to be unraveled. In this paper, we take mitochondrial mechanobiology as an example to discuss recent advances and current technical challenges in this field. In addition, we discuss the needs for future toolbox development for mechanobiological research of intracellular organelles.