Mounds constructed by Cinctipora elegans in Foveaux Strait have been seriously damaged as a result of trawling for oysters. This is particularly unfortunate because those oysters living in the bryozoan mounds are less vulnerable to outbreaks of the parasitic protist Bonamia exitiosa.

The main threat to the survival of Cinctipora elegans itself probably comes from ocean acidification that may make construction of its calcium carbonate skeleton difficult.