Coral bleaching involves the loss of essential photosynthetic dinoflagellates (Symbiodinium sp.) from host gastrodermal cells in response to temperature or light stress. Although numerous potential cellular bleaching mechanisms have been proposed, there remains much uncertainty regarding which cellular events occur during early breakdown of the host–dinoflagellate symbiosis. In this study, transmission electron microscopy was used to conduct a detailed examination of symbiotic tissues of the tropical anemone Aiptasia pallida during early stages of host stress. Bleaching was induced by exposing specimens to a stress treatment of 32.5±0.5°C at 140±7 µ mol photons m^–2 s^–1 light intensity for 12 h, followed by 12 h at 24±1°C in darkness, repeated over a 48 h period. Ultrastructural examinations revealed numerous dense autophagic structures and associated cellular degradation in tentacle tissues after ∼12 h of the stress treatment. Anemones treated with rapamycin, a known autophagy inducer, exhibited the same ultrastructural characteristics as heat-stressed tissues, confirming that the structures observed during heat stress treatment were autophagic. In addition, symbionts appeared to be expelled from host cells via an apocrine-like detachment mechanism from the apical ends of autophagic gastrodermal cells. This study provides the first ultrastructural evidence of host autophagic degradation during thermal stress in a cnidarian system and also supports earlier suggestions that autophagy is an active cellular mechanism during early stages of bleaching.