Habitat loss due to land reclamation often occurs in sandy coral reef shore zones. The giant sea anemone Stichodactyla gigantea, which harbors the false clown anemonefish Amphiprion ocellaris, both of which are potentially flagship species, inhabit these places. To assess habitat quality for S. gigantea, we examined correlative associations between the number and the body size of S. gigantea and the amount of habitat types in fine-scale seascape composition quantified from an enlarged section of a high-resolution (1/2,500) color aerial photograph of the shallow shore zone of Shiraho Reef, Ishigaki Island, Japan. This study confirmed that anemones were most abundant at the edges of dense seagrass beds characterized by shallow sandy bottoms, rock beds, and sparse seagrass beds, while they were less abundant in coral patch reefs. However, anemones inhabiting coral patch reefs were significantly larger and their rate of disappearance over 3 years was lower than those inhabiting other habitats. This suggests that coral patch reefs may be more suitable habitats supporting larger animals and greater persistence of S. gigantea. The visual census techniques applied here, combined with aerial photography and image-analysis software, may be useful as a simple analytical tool for local assessment of suitable habitats for relatively small-bodied marine fauna in shallow-water seascapes.