Studying the morphological changes of zooxanthellae in the host gastroderm is essential to understand the mechanisms of bleaching. Transmission electron microscopy was used to observe samples from four coral species – three collected from a barrier reef in Madagascar (Acropora digitifera (Dana, 1846), Echinopora hirsutissima Milne-Edwards & Haime, 1849 and Porites (Synaraea) rus Forskål, 1775)) and one cut from an aquarium-grown coral (Pocillopora damicornis (Linnaeus, 1758) − and from the hermatypic (zooxanthellae-containing) sea anemone Aiptasia pulchella (Carlgren, 1943). Zooxanthellae from bleached animals showed different stages of degradation or disorganization. Some were free, detached from the host gastroderm, associated or not with host-cell remains. Others were vacuolated, with abundant reserve material globules and angular holes probably created by the loss of crystalline material during cutting. Experimentally heat-shocked P. damicornis harboured, moreover, a greater number of dividing algae. Bleached individuals were found to vary as regards their response to stress, and zooxanthellae expelled from heat-shocked anemones showed a greater mitotic index and a higher survival rate than algae extracted or naturally externalized from healthy individuals. We propose a combination of morphological criteria for use in diagnosing the health state of algae-cnidarian symbiosis, so vulnerable in the case of bleaching.