Pyrenoids are sub-cellular micro-compartments found in chloroplasts of many algae, and in a single group of land plants, the hornworts. Pyrenoids are associated with the operation of a carbon-concentrating mechanism (CCM). Their main function is to act as centres of carbon dioxide (CO₂) fixation, by generating and maintaining a CO₂ rich environment around the photosynthetic enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Pyrenoids therefore seem to have a role analogous to that of carboxysomes in cyanobacteria.

Algae are restricted to aqueous environments, even in aquatic habitats, and this has implications for their ability to access CO₂ for photosynthesis. CO₂ diffuses 10,000 times slower in water than in air, and is also slow to equilibrate. The result of this is that water, as a medium, is often easily depleted of CO₂ and is slow to gain CO₂ from the air. Finally, CO₂ equilibrates with bicarbonate (HCO₃⁻) when dissolved in water, and does so on a pH-dependent basis. In sea water for example, the pH is such that dissolved inorganic carbon (DIC) is mainly found in the form of HCO₃⁻. The net result of this is a low concentration of free CO₂ that is barely sufficient for an algal RuBisCO to run at a quarter of its maximum velocity, and thus, CO₂ availability may sometimes represent a major limitation of algal photosynthesis.