Fossil reefs have the potential to provide important data for studies of climate and environmental change. This is particularly true for Pleistocene-Holocene coral reefs, which predominantly consist of communities undisturbed by anthropogenic impact and therefore provide a baseline for evaluating the status of modern reefs. We used photo transects and point-counting to quantitatively compare two Pleistocene reef terraces of two Pleistocene sites, tentatively assigned to marine isotope stage 5e, with habitats (reef flat, reef edge, reef slope at 5- and 10-m water depth) of a modern reef near El Quseir, Egypt. The modern reef exhibits a clear trend of increasing taxonomic richness and diversity from the reef flat towards the reef slope at 10-m water depth. The most abundant genera are Pocillopora, Acropora, Millepora, and massive Porites, but strong differences between individual habitats were evident. The most abundant genera in the fossil reefs are massive Porites and Dipsastraea. With regard to quantitative composition, all modern reef habitats differed significantly from each other as well as from the fossil reefs. The fossil reef composition is most similar to the modern reef slope habitat at 10-m water depth. There are two conflicting hypotheses on geodynamic processes for this area—these are tectonic uplift and tectonic stability. Considering tectonic stability, the fossil reefs would have to be interpreted as lagoonal patch reefs, for which no modern counterparts exist in the study area. However, in the case of tectonic uplift, we conclude that the fossil reefs studied were once situated at around 10-m water depth.