Diazotrophs are an important symbiotic partner of corals and they can supplement the coral holobiont nitrogen budget by generating biologically usable form of nitrogen. In this study, we investigated the diversity of diazotrophic bacterial communities associated with coral Pocillopora damicornis in conditions of increased temperature seawater by profiling the conserved subunit of the nifH gene, which encodes the dinitrogenase iron protein. The diazotrophic bacterial communities are significantly different related to environmental conditions and coral health status.This study provides broad insight into the improvement of the fitness of corals during thermal stress.