Many marine calcifiers engage in obligatory algal symbiosis which is threatened by ocean warming, jeopardising the critical support it provides to the holobiont. Large benthic foraminifera are prominent carbonate and sand producers in shallow environments with a wide range of species-specific thermal tolerances assumed to be related to their diverse algal symbionts. We examine two diatom-bearing benthic foraminifera species which differ in their thermal physiological tolerance and symbiont community composition. Our findings demonstrate that the less thermally-tolerant host, A. lobifera, ‘shuffles’ the dominant players of the internal symbiont community with increasing temperature while the more thermally-tolerant host P. calcariformata is dominated by Arcocellulus cornucervis at all temperatures. Although this diatom species was present in A. lobifera from all treatments, it became more abundant only under the most severe temperature stress. Symbionts were isolated from the thermally-tolerant foraminifera P. calcariformata, with only one species surviving at 35?C, while the others failed to survive at 32?C. Supplementation of isolated symbionts increased the ability of A. lobifera to recover from bleaching under heat stress suggesting that while increased temperature creates shuffling at the family level, heat tolerance of the holobiont is related to changes at the species level of the symbiont algae.