In the past 1.5 billion years, mitochondria have evolved from oxygen-scavenging bacterial symbionts into primary control centers for energy production and cellular life-and-death processes in eukaryotes. This maturation of mitochondrial function has necessitated the coevolution of various mechanisms of communication with the rest of the cell. Emerging evidence indicates that reversible phosphorylation, the most prevalent form of cellular posttranslational modification, is an important and largely overlooked means of regulating mitochondrial functions. The steadily increasing number of reported mitochondrial kinases, phosphatases and phosphoproteins suggests that phosphorylation is likely to emerge as a common theme in the regulation of mitochondrial processes.