Mitochondria are pleiotropic regulators in metabolic pathways, calcium and redox homeostasis, and apoptosis. These diverse mitochondrial functions are reflected by their extremely dynamic morphology and distribution in the cells. Mitochondrial quality, distribution, size, and motility are excellently tuned by their continuous fusion and fission. Stem cells are special cell population with self-renewal and differentiation potentials. Healthy stem cells contribute to tissue maintenance and repair, while tumour stem-like cells commit tumour malignancy, such as recurrence, drug resistance, and metastasis. We are focusing on mitochondrial dynamics in stemness maintenance as well as differentiation of healthy, and tumour cells.