Change occurring in Chlamydomonas reinhardtii as cells adapt to limiting CO2 conditions were examined at both a molecular level and an ultrastructural level. It was demonstrated using antibodies that the time course of the de novo synthesis of LIP-21, a 21 kD limiting-CO2 induced polypeptide, correlates with the appearance of CO2 concentrating activity and that expression of the nuclear gene for LIP-21 is regulated at the level of translatable message. These results are consistent with LIP-21 being a component of an adaptive response to limiting CO2, such as the induction of the CO2 concentrating mechanism. Phase separation of membrane proteins indicated that both LIP-21 and LIP-36, an induced 36 kD protein, were probably peripheral membrane proteins, possibly part of a protein complex in the membranes;Immuno-gold labeling was used to localize LIP-21 antibody was specifically to mitochondria in air-adapted cells. This is of particular significance because there is a relocation of these mitochondria upon transfer to limiting CO2, from positions predominantly in the central portion of the cells to peripheral positions between the chloroplast envelope and the plasmamembrane. Although not necessarily related, these two observations do suggest a role for the mitochondria in the adaptive response. Possible functions that might served more optimally in the peripheral position include glycolate scavenging, supply of ATP for active transport, or elimination of excess reductant. LIP-21 might possibly be involved with any of these hypothesized functions, or it might facilitate the relocation of the mitochondria;Other ultrastructural changes observed upon transfer to limiting CO2 include a transient decline in the level of stromal starch, apparently dependent on the immediate availability of carbon, while pyrenoid starch sheath accumulation which remains present in the air-adapted state. It has been speculated that the starch sheath could serve as a diffusion barrier to prevent loss of CO2 from the pyrenoid. The pyrenoid itself does not appear to develop further in air-adapted cells, in contradiction to earlier reports. There is also an increase in the degree of vacuolization upon transfer to limiting CO2 levels. It is not clear what function this might serve.