Intertidal mangrove wetlands are of great economic and ecological importance. The regular influence by tide leading to the microbial communities in these wetlands differs significantly from other habitats. The effect of anthropogenic activity that protecting mangrove wetlands from tide on the microbiomes are not understood. In this study, we investigate mangrove species related microbiomes in protected (Bamen Bay) and natural intertidal wetlands (Dongzhai Bay) from two mangrove wetlands in Hainan Island. Soil samples from 13 mangrove species root zone were collected. Microbial composition was assessed using Illumina sequencing. Our bioinformatics analyses indicate that microbiomes shifted significantly between mangrove wetlands with and without anthropogenic protection. In protected site, microbiomes were more similar to those of terrestrial and freshwater ecosystems, whereas in natural site were more related to marine and other intertidal wetlands. The overall microbiome was assigned into 78 phyla and Proteobacteria is the most abundant group in both sites at phylum level. At class level, however, an even distribution of Alph, Beta, Gamma and Delta Proteobacteria was found in Bamen Bay, whereas the Gamma and Delta Proteobacteria were more dominant in Dongzhai Bay. Functional consortia of sulfate reducing bacteria (SRB) was mostly occurred in Dongzhai Bay nitrite oxidizing bacteria, ammonia oxidizing arhea (AOA) were major groups in nitrification process the relative abundances of methanogens and methanotrophs were not exceed 1%, indicating a weak methane generation and oxidation in both sites. We also observed distinct microbial compositions among mangrove species in Bamen Bay. Our data suggest that mangrove species and pH are main factors influence microbiomes in protected mangrove wetland.