Archaea communities widely exist in mangrove forest sediments, but their spatial variations among different distribution areas with salinity gradient in mangrove forest sediments is not well understood. This study used 16S rRNA Miseq sequence to investigate the sediment archaeal community structure and diversity of Bruguiera gymnoihiza mangrove forest in China along three different distribution areas. The results showed rich methanogen and ammonia-oxidizing archaea resources in the study site, with Methanobacterium, Methanothrix, Methanomassiliicoccus, Nitrosopumilus and Nitrososphaera (>1%) as the dominant genera. Mantel test and Redundancy analysis (RDA) results revealed that pH was the determinant for archaeal community structure in our study. The RDA result showed that the available K also contributed to archaeal community structure. There was a significant and positive relationship between pH and available P; in addition, the two values were significantly and negatively related to the observed OTU number. These results suggested that pH is the main determinant of the archaeal community structure and diversity in distribution areas of Bruguiera gymnoihiza in Dongzhaigang.