Chloroplasts have evolved a complex proteinaceous machinery to import nuclear-encoded proteins. The origin of this machinery, following the endosymbiotic events leading to chloroplasts, is an intriguing, unresolved problem. Given that cyanobacteria are the probable ancestors of chloroplasts, the genome sequence of Synechocystis sp. PCC 6803 offers a valuable resource to identify putative homologs for components of this protein import machinery and to gain insights into its possibly endosymbiotic origin. Detailed computational sequence analysis reveals that Synechocystis sp. PCC 6803 has homologs of three of the known membrane proteins of the chloroplastic translocon, namely Toc75, Tic20 and Tic22, as well as a homolog of the putative component Tic55. Thus, the chloroplastic protein import machinery is mainly derived from the endosymbiotic cyanobacterium, but, interestingly, not from any of the four main protein secretion systems of prokaryotes. The relatively high sequence variability between chloroplastic and Synechocystis proteins suggests that the ancestral proteins had different physiological roles and were modified significantly to fulfill the new demand of importing proteins into the evolving chloroplast. The fact that some chloroplastic protein import components are not related to any Synechocystis proteins (Toc159, Tic110 and Toc34) indicates that the chloroplastic protein import apparatus is of a dual evolutionary origin.