Millepora, a hydrozoan coral, is a common component in modern tropical reefs throughout the world. In ecological and palaeoecological surveys it is often grouped with scleractinian corals, which are the prevailing builders of coral reefs. On modern, current-exposed reefs in the Red Sea, Millepora can become the dominant coral. However, it is rarely found in fossil reefs and if present, its abundance is usually considerably lower than in modern reefs. The mismatch is often explained by a low preservation potential of the milleporid skeleton in the fossil record. We explore Millepora abundances in Pleistocene reefs of Egypt using 29 line transects (typically of 20 m length), and find its abundances to be comparable to that of adjacent modern reefs (between 0 and 18.8 ± 8.5 % per site). Comparisons between sites with and without Millepora suggest that site specific environmental characteristics determine the presence of Millepora in the fossil reef. We conclude that a lack of preservation of habitats preferred by Millepora instead of the preservation potential of the hydrozoan itself is the most plausible reason for the mismatch between modern and fossil abundances.