Considering that Protopalythoa species inhabit coral reefs, it is safe to assume that they would be at threat from the same processes that affect coral reefs as an entire ecosystem. Global warming would most likely have a significant effect on these species, as the presence of symbiotic zooxanthellae is known to be affected greatly by temperature. 

Due to the lack of research and knowledge regarding the species within this genus and the genus Palythoa, it cannot be speculated what factors threaten these species until further research is undertaken.