"Cyanelles" are peptidoglycan-armored plastids of glaucocystophyte algae with close morphological and biochemical resemblance to endosymbiotic cyanobacteria. Genome sequencing and phylogenetic analysis have placed cyanelles on the earliest branch of phototrophic eukaryotes after the singular primary endosymbiotic event, the closest relatives to cyanobacteria among extant plastids. This model is supported by similar mechanisms for the targeting of nucleus-encoded cyanelle and chloroplast precursor proteins whose genes were transferred to the nucleus after the endosymbiotic event. As in chloroplasts, a prokaryote-type Sec preprotein translocase is shown to operate in cyanelle thylakoid membranes.