The sea anemone Entacmaea quadricolor simultaneously harbours multiple symbiont types from the genus Symbiodinium, while providing essential habitat for anemonefish. This anemone lives close to its upper thermal threshold and experiences bleaching under elevated temperature and light stress. Here, we determine whether E. quadricolor experienced a shuffling in the abundance of two genetically distinct symbiont types (Symbiodinium C25 and C3.25) during bleaching and recovery. Anemones were exposed to control (22.9 °C) or elevated temperature (28.5 °C) for 42 days, whereas for the following 75 days, all anemones were exposed to 22.9 °C. By day 47, a more pronounced bleaching occurred via symbiont expulsion in the elevated temperature treatment than the control, and the proportion of C25 to C25 + C3.25 increased by 6.2 and 13.2 % in the control and bleached anemones, respectively. The increased relative abundance of C25 to C3.25 after exposure to thermal stress may indicate that C3.25 performs poorly when temperature is elevated. Although no significant recovery in symbiont density was detected, a revival of the C3.25 genotype was found at day 117, which may indicate that it is either more competitive or has qualities that are beneficial to the symbiosis when thermal stress is no longer apparent. This work demonstrates the potential for this anemone species to shuffle its symbiont types in response to environmental change and could provide resilience during times of stress.