Protein phosphorylation by [gamma-32P]ATP in total extract and subfractions of bovine heart mitochondria has been studied. The results show that, in addition to pyruvate dehydrogenase, three mitochondrial proteins, with molecular weights of 44,000, 39,000 and 31,000 Da, are phosphorylated by a cAMP-independent mitochondrial protein kinase. Three other proteins associated with mitochondria, with molecular weights of 125,000, 19,000 and 6,500 Da, are phosphorylated by the cytoplasmic cAMP-dependent protein kinase (kinase A).