Eukaryotic autotrophs, generally assembled as plants, are polyphyletic and they appear across at least five super groups of eukaryotes, which indicate that photosynthesis has been horizontally transferred between different lineages of eukaryotes. This situation is explained by secondary endosymbioses that should have occurred between heterotrophic eukaryotes and primary plants (red and green algae). Evolutionary process generating new algal lineage can be considered by comparison of dinoflagellates and Hatena, a flagellate we recently found, all of which are likely under intermediate stages of secondary endosymbioses. Evolution of protein transport machinery to send nuclear encoded proteins back into the plastids was also considered referring recent reports of molecular biology.