Cnidarians containing symbiotic microalgae often inhabit highly variable light environments where successful growth requires that, during transient (potentially stressful) periods of high light (HL), the microalgal cells invest energy in photoprotection to minimise photodamage, or allow for photodamage to occur and invest in photorepair; however, the relative contribution of photoprotection and photorepair remains uncharacterised. Here we determined the light dependence of Photosystem II (PSII) photoinhibition and photorepair in 2 phylotypes of Symbiodinium displaying different susceptibilities to thermal stress. Upon exposure to photon flux densities (PFDs) >500 µmol photons m–2 s–1 the thermally ‘sensitive’ Strain A1.1 displayed higher net photoinhibition, measured as a decrease in maximum PSII efficiency (Fv/Fm), than the thermally ‘tolerant’ Strain A1. In contrast, gross photoinhibition, assessed as the decline of Fv/Fm in the presence of an inhibitor of D1 protein synthesis, was similar in the 2 strains. Therefore, photorepair was considered to be the key mechanism minimising net photoinhibition in Strain A1. Consistent with this conclusion, the 2 strains displayed similar capacities for other mechanisms of avoiding photodamage, specifically, photochemical (qP) and non-photochemical (NPQ) excitation energy quenching. Measurements on Strain A1 grown under 2 PFDs (100 and 650 µmol photons m–2 s–1) revealed that photoacclimation to HL involved the upregulation of qP, which minimised gross photoinhibition by maintaining PSII in a more oxidised state. We conclude that both interspecific (e.g. phylotype diversity) and intraspecific (e.g. photoacclimation state) factors affect the susceptibility of Symbiodinium to light stress.