We examined the utilization of carbon and nitrogen in two common Red Sea coral species (Stylophora pistillata and Favia favus), differing in colony morphology and polyp size, along a depth gradient down to 60 m. We describe the changes in C/N ratios and in the stable isotope composition of carbon and nitrogen of coral’s tissue and algal symbionts. We also measured the carbon isotopic composition of the lipid fraction extracted from both coral tissue and algal symbionts in order to reveal the changes in the carbon source utilized by the host coral for lipid synthesis. The results show that for both species, d13C decreases by 7–8‰ in animal tissue, algal symbionts and in the lipid fractions as depth increases. However, in contrast to previous reports, the difference between d13C values of coral tissue and algal symbionts does not increase with depth. d15N values of coral tissue and algal symbionts in both species do not correlate with depth suggesting that the heterotrophic capacity of these corals does not increase with depth. d13C values of tissue lipids were depleted by an average of ~3.5‰ compared to d13C of the entire tissue at all depths. d13C values of algal lipids were depleted by an average of ~2‰ compared to d13C of the entire zooxanthellae at all depths, indicating high efficiency of carbon recycling between the two symbiotic partners along the entire gradient. The depletion of lipids is attributed to the fractionation mechanism during lipid synthesis. In addition, for both species, d13C values of algal lipids were enriched compared with d13C of tissue lipids. In S. pistillata, the difference between d13C values of tissue lipids and algal lipids increased linearly with depth, indicating a change in the sources of carbon utilized by the coral for lipid synthesis below 20 m from an autotrophic to a heterotrophic source. However, in F. favus, this average difference was ~4 times larger compared to shallow S. pistillata and was constant along the entire depth gradient, suggesting that F. favus uses heterotrophically-acquired carbon for lipid synthesis regardless of depth. Overall, F. favus exhibited enriched d13C and d15N values compared to S. pistillata along the entire gradient. We attribute these differences to both morphological differences (i.e. colony morphology, tissue thickness and polyp size) between the two species and to a higher heterotrophy/autotrophy ratio in F. favus at all depths. The C/N ratio in S. pistillata tissue decreased with increasing water depth whereas in F. favus it remained constant. This reflects a higher hetero- trophic capacity in the large polyped F. favus, at all depths.