The genome of Saccharomyces cerevisiae contains as many as 136 protein kinase encoding genes. However, only a limited number of mitochondrial protein kinases have been characterized. A computer-aided analysis revealed that only seven members of this large protein family are potentially localized in mitochondria. The low abundance of mitochondrially targeted protein kinases in yeast reflects the reductive evolution of mitochondrial signaling components and/or the apparent lack of selection pressure for acquiring mitochondrially localized protein kinases encoded by the host genome. This suggests that mitochondria, like obligatory intracellular bacterial parasites, are no longer dependent on signalling mechanisms mediated by protein kinases residing within the mitochondria. Instead, the nucleo-mitochondrial communication system requiring protein phosphorylation may be predominantly regulated by protein kinases, which are cytosolic and/or anchored to the outer mitochondrial membrane.