Photosynthesis produces chemical energy from photon energy in the photosynthetic electron transport and assimilates CO2 using the chemical energy. Thus, CO2 limitation causes an accumulation of excess energy, resulting in reactive oxygen species (ROS) which can cause oxidative damage to cells. O2 can be used as an alternative energy sink when oxygenic phototrophs are exposed to high light. Here, we examined the responses to CO2 limitation and O2 dependency of two secondary algae, Euglena gracilis and Phaeodactylum tricornutum. In E. gracilis, approximately half of the relative electron transport rate (ETR) of CO2-saturated photosynthesis was maintained and was uncoupled from photosynthesis under CO2 limitation. The ETR showed biphasic dependencies on O2 at high and low O2 concentrations. Conversely, in P. tricornutum, most relative ETR decreased in parallel with the photosynthetic O2 evolution rate in response to CO2 limitation. Instead, non-photochemical quenching was strongly activated under CO2 limitation in P. tricornutum. The results indicate that these secondary algae adopt different strategies to acclimatize to CO2 limitation, and that both strategies differ from those utilized by cyanobacteria and green algae. We summarize the diversity of strategies for prevention of photo-oxidative damage under CO2 limitation in cyanobacterial and algal photosynthesis.