The health and productive of coral reef worldwide are recently threatened by the bleaching phenomenon that describe the breakdown of the delicate association of corals and their phototrophic endosymbionts. The molecular processes in the corals during the bleaching event are still incompletely understood but complex gene expression changing has been observed. Histone gene variants are modified canonical histone genes that pack the DNA to nucleosomes immediately after replication. The replacement of canonical histones by histone variants can alter gene expression in a complex manner. In this study, the characterization and gene expression of two histone variants, macroH2A and H2A.Z, will be investigated in several natural populations of scleractinian corals from the Hainan Island (South China Sea) allowing well-founded estimations about the impact and role of these genes in the bleaching phenomenon. This will be the first comprehensive analysis of gene expressions in natural coral population and the characterization of these genes from corals as basal members of metazoan. Thus, this study will provide insights in histone gene evolution within metazoan and will be an important part for the detailed understanding of the molecular process takes place in natural population of corals in response to environmental changing e.g. during the bleaching phenomenon.