In summer 1998, shallow water corals at Sesoko Island, Japan (26°38′N, 127°52′E) were damaged by bleaching. In August 2003, partially damaged colonies of the massive Porites lutea and the branching P. cylindrica were collected at depths of 1.0–2.5 m. The species composition of epilithic algal communities on dead skeletal surfaces of the colonies (‘red turfs’, ‘green turfs’, ‘red crusts’) and the endolithic algae (living in coral skeletons) growing close to and away from living coral polyps was determined. Carbon and nitrogen stable isotope values of organic matter (δ¹³C and δ¹⁵N) from all six of these biological entities were determined. There were no significant differences in the isotope composition of coral tissues of the two corals, with P. lutea having δ¹³C of −15.3 to −9.6‰ and δ¹⁵N of 4.7–6.1‰ and P. cylindrica having similar values. Polyps in both species living close to an interface with epilithic algae had similar isotope values to polyps distant from such an interface. Despite differences in the relative abundance of the algal species in red turfs and crusts, their δ¹³C and δ¹⁵N values were not significantly different from each other (−18.2 to −13.9, −20.6 to −16.2, 1.1–4.3, and 3.3 to 4.9‰, respectively). The green algal turf had significantly higher δ¹³C values (−14.9 to −9.3‰) than that of red turfs and crusts but similar δ¹⁵N (1.2–4.1‰) to the red algae. The data do not suggest that adjoining associations of epilithic algae and coral polyps exchange carbon- and nitrogen-containing metabolites to a significant extent. The endolithic algae in the coral skeletons had δ¹³C values of −14.8 to −12.3‰ and δ¹⁵N of 4.0–5.4‰. Thus they did not differ significantly from the coral polyps in their carbon and nitrogen isotope values. The similarity in carbon isotope values between the coral polyps and endolithic algae may be attributed to a common source of CO₂ for zooxanthellae and endolithic algae, namely, from respiration by the coral host. While it is difficult to fully interpret similarity in the nitrogen isotope composition of coral tissue and of green endolithic algae and the difference in δ¹⁵N between green epilithic and endolithic algae, the data are consistent with nitrogen-containing metabolites from the scleractinian coral serving as a significant source of nitrogen for the endolithic algae.