Mitochondria and plastids are the result of independent endosymbiotic events. While these organelles harbour their own genome, they are required to import the majority of their proteome from the cytosol. Theory has it that protein import into the mitochondrial matrix depends on the presence of N-terminal targeting sequences (NTS) on the majority of proteins that acts as a ligand for a receptor of the outer mitochondrial membrane. However, the conservation of NTS- independent targeting in some protists suggest the ancestral mode of mitochdonrial targeting not only differed, but has also been retained. After the acquisition of plastids subsequent to the mitochondrium, protein targeting to the plastids evolved in the presence of mitochondrial targeting, a crucial aspect of which was avoiding mislocalization. Although the import machineries of the two organelles share remarkable functional similarities, plastid NTSs contain sufficient information to prevent targeting to mitochondria. The growing list of proteins that are dual targeted to both organelles thins out the list of features unique for the NTSs of each organelle. One unique character remaining is charge. Positive charges on mitochondrial targeting sequences are selected during evolution due to the presence of ∆ψ. Here we look at organisms with primary and secondary plastids in addition to mitochondria and discuss the crucial role of charge as a determining feature of organellar protein targeting.