In all higher plants and algae, photosynthetic processes are localized in organelles called chloroplasts. In plants, most of the chloroplasts are found in cells just under the leaf surface (mesophyll cells). Each cell may contain 20 to 50 of these organelles. The eukaryotic algae also have chloroplasts, but often only one very large one is found in each cell.

Like mitochondria, chloroplasts are semiautonomous, carrying their own DNA to code for some of their proteins, as well as the ribosomes necessary for translation of the appropriate messenger RNAs. There is now much evidence that chloroplasts evolved from unicellular organisms similar to cyanobacteria (blue-green algae). Such prokaryotic photosynthesizers do not contain chloroplasts but have membrane structures that play the same roles as chloroplast membranes. To a certain extent, the cyanobacteria resemble free-living chloroplasts. It is believed that, early in evolution, primitive unicellular organisms took up cyanobacteria-like prokaryotes and that eventually the relationship became symbiotic: The photosynthetic organelles were no longer capable of independent life, and the algae depended upon them as energy sources.

Some chloroplast genes are coded in the organelle genome, and some are in the cell nucleus.