Coral larvae and juveniles often exhibit green fluorescence due to green fluorescence proteins (GFP). Ontogenetic changes in the distribution pattern of green fluorescence in coral are not fully understood. We investigated changes in the intensity and distribution pattern of green fluorescence of the corals Acropora tenuis, Pocillopora damicornis, and Isopora palifera during early developmental stages. Green fluorescence distribution in larvae differed among the three species studied and changed after the larvae metamorphosed into primary polyps. Green fluorescence distributed mainly in the epidermis of P. damicornis and I. palifera larvae but in the gastrodermis in A. tenuis larvae. In P. damicornis and A. tenuis primary polyps, green fluorescence was present around the oral opening and in a ring structure below the tentacular ring. Green fluorescence was also present on the tips of the tentacles of P. damicornis and I. palifera primary polyps. Furthermore, green fluorescence intensity in A. tenuis primary polyps increased significantly after inoculation of symbionts, irrespective of the success of symbiont acquisition. In I. palifera, the fluorescence intensity decreased and, in some cases, disappeared after the acquisition of symbionts. Moreover, bleaching stress increased green fluorescence in P. damicornis juveniles. The present observations suggest that green fluorescence intensity in juvenile corals is influenced by the presence or acquisition of symbiont cells as well as by stressful conditions. This study also suggests that GFP might have different functions among coral species and at different developmental stages of the corals.