Mitochondria fulfill central cellular functions including energy metabolism, iron-sulfur biogenesis, and regulation of apoptosis and calcium homeostasis. Accumulation of dysfunctional mitochondria is observed in ageing and many human diseases such as cancer and various neurodegenerative disorders. Appropriate quality control of mitochondria is important for cell survival in most eukaryotic cells. One important pathway in this respect is mitophagy, a selective form of autophagy which removes excess and dysfunctional mitochondria. In the past decades a series of essential factors for mitophagy have been identified and characterized. However, little is known about the molecular mechanisms regulating mitophagy. The role of mitochondrial dynamics in mitophagy is controversially discussed. Here we will review recent advances in this context promoting our understanding on the molecular regulation of mitophagy in Saccharomyces cerevisiae and on the role of mitochondrial dynamics in mitochondrial quality control.