Plastids are a diverse group of plant organelles involved in numerous important biological processes including photosynthesis, sensing gravity, storing fats, oils, pigments and proteins, as well as synthesizing monoterpenes, starch and fatty acids. The structures and functions of plastids are wide-ranging both within a single plant as well as between different species; however, this diversity has been almost overlooked at the protein level due to the reliance of plastid research upon a small number of model organisms such as Arabidopsis thaliana, Nicotiana tabacum, and Solanum lycopersicum. In an effort to generate predicted plastid proteomes for economically important crops, the Malus x domestica Borkh. (apple) genome was analyzed via two different methods, a custom analysis and a TargetP-based analysis, to identify putative plastid targeted proteins. These predicted proteins were compared with plastid targeted proteins described by the Arabidopsis Chloroplast 2010 project. Genes unique to and shared between apple and Arabidopsis were annotated using Blast2GO to determine putative protein functions, biological processes, and cellular location. Both analyses identified roughly 20% of the genes within apple to encode plastid-targeted products. Of these, 2,290 genes had no known plastid-targeted homologues in A. Thaliana and 1,014 did not have a homologue in the NR database as identified by BLASTX. Further documentation of the differences of plastid proteomes throughout the plant kingdom will aid in finding new and novel plastid processes.