Environmental microbiota plays a vital role in the intestinal microbiota of aquatic organisms. However, data concerning the association between intestinal microbiota of pearl oyster and surrounding seawater are limited. Existing bacterial communities in the pearl oyster Pinctada fucata martensii intestine and surrounding water from two sites were investigated by using a 16S rRNA-based sequencing to explore the relationship amongst the two. Results revealed the richness and diversity of pearl oyster intestinal microbiota to be less than those of the surrounding water, with 38 phyla and 272 genera observed as a result of the classifiable sequence. The microbiota compositions in the intestine and the surrounding water were diversified at the phylum and genus levels with the sequencing data being statistically significant. However, the inferred metagenomics emphasizes on the overall similarity in the functional profile of the surrounding seawater and intestinal microbiomes. This profile was associated to the metabolism of amino acid, carbohydrate, and energy, and membrane transport. Seven common operational taxonomic units (OTUs), which belong to the phylum Tenericutes, Cyanobacteria, and Planctomycetes, were noted in the intestines of pearl oysters from two different sites. These OTUs may be affiliates to the core microbiome of pearl oyster. Significantly different bacterial taxa in the intestines of pearl oysters from two different sites were found at the phylum and genus levels. This finding suggests that bacterial communities in pearl oyster P. f. martensii intestines may exhibit some plasticity to adapt to changes in the surrounding water-cultured environment. Generally, our study offers constructive discoveries associated with the pearl oyster intestinal microbiota and provide guidance for sustainable aquaculture.