Coral reefs represent one of the richest ocean micro-scale environments that include diverse collection of both basic and advanced species.Analysis of the microbial communities that live with coral reefs could help to answer key ecological questions about coral symbionts.The connection of community structure and the environmental factors would also provide clues for important chemical cycling.In this work, we have collected sequencing data of coral symbiont microbial communities collected from two distinct geological locations: the South China Sea and Moorea.A number of 25 coral reefs samples were collected and categorized into 7 groups: Porites Iutea, Galaxea fascicularis, Acropora millepora, Paopao Bay,Fore reef, back reef, and Fringing reef, from the datasets downloaded from NCBI (SRR82519 and SRP007926).The number of reads ranged from 554 to 23,858 in each sample.Firstly, 199,860 reads were remained after quality filtering and clustered into 2149 different OTUs.Trimmed sequences were grouped into 31 high-level taxonomic groups at the phylum level.Secondly, the microbial communities from these two locations were largely different and the species with different abundances, especially Cyanobacteria, was found to be indicators that could reflect human activities and coral reefs health status.Three dominant phyla (Proteobacteria, Firmicutes, and Bacteroidetes) comprised 58.6% and 71.0% of the P1 and Gf communities,respectively.However, for Am, three dominant phyla (Proteobacteria, Firmicutes, and Deinococcus-Thermus)comprised 97.3% of the communities and 2 predominant phylum (Proteobacteria and Cyanobacteria)comprised 80.95% of the A, B, C, D, E and H sites on average.Thirdly, the results of NMDS, PCoA, and clustering analysis showed that these samples could be divided into three groups: Am group (from South China Sea), Moorea group, and P1+Gf group (from South China Sea), and the results were consistent with the results of Kruskal-Wallis test.Fourthly, based on Kruskal-Wallis test among classes and the pairwise Wilcoxon test among subclasses, 28 taxon were chosen as biomarkers using LEfSe pipeline, such as Prochlorococcus of Moorea, Rhodopirellula of P1+Gf, and Deinococcus of Am.Furthermore, we have generally listed pathogens that may be associated with coral reef diseases, for example, Vibrio genus and Thalassomonas genus.In summary, the metagenomic sequencing study of coral symbionts can serve as an efficient and effective approach for monitoring of coral reefs wellness.