Molecular recognition of N-terminal targeting peptides is the most common mechanism controlling the import of nuclear-encoded proteins into mitochondria and chloroplasts. When experimental information is lacking, computational methods can annotate targeting peptides, and determine their cleavage sites for characterizing protein localization, function, and mature protein sequences. The problem of discriminating mitochondrial from chloroplastic propeptides is particularly relevant when annotating proteomes of photosynthetic Eukaryotes, endowed with both types of sequences.