Effects of temperature on carbon fixation rates and partitioning between Aiptasia pallida (Verrill) and its symbiotic alga Symbiodinium microadriaticum Freudenthal were examined by ¹⁴C incubation studies. Total fixation varied strongly with temperature, with an optimum of 32 °C. More photosynthate was translocated to the host at 12 °C (82%) than at 27 °C (63%). Partitioning among three fractions (alcohol soluble, ether soluble, and alcohol/ether insoluble) varied with temperature in Aiptasia pallida, but not in the alga. Relative partitioning between host and alga increased with time in favor of A. pallida when maintained at 12 °C, but absolute levels of translocation to the host did not change; however, photosynthate retention by the alga did decline substantially. Total fixation declined by ≈ 80% after 10 days at 12 °C. Turnover rates of fixed carbon also varied with temperature, as determined by pulse-chase studies, and the effect varied for the different fractions. These results suggest that zooxanthellae are less thermally adaptable than their hosts, and may be especially susceptible to low temperatures. Thermal effects on biochemical partitioning may have great importance in relation to growth and reproduction of animal hosts of zooxanthellae and the viability of the symbiotic relationship. These effects, combined with the pronounced effect of temperature on total photosynthate production, probably play a major role in limitation of zooxanthellal symbioses to warm waters.