Filter-feeding bivalves provide habitats for microbial colonization. Microbes also affect the growth and development of host organisms. Mytilus coruscus not only has economic importance in China but also shows powerful immune tolerance to environmental changes. However, the underlying tissue-specific pattern of microbial communities of M. coruscus is still poorly understood. To fill these knowledge gaps, we collected 7 tissues of M. coruscus cultured in Shengsi breeding area. These tissues included hemolymph, digestive glands, kidneys, gills, mantles, gonads and feet. Through the 16S rRNA gene amplicon sequencing targeting the V3-V4 variable region on the Illumina MiSeq platform, we characterized the community structure and distribution of microbiota. On average, a total of 36 860 high-quality reads were obtained from 21 samples of M. coruscus. The highest number of OTU (1 237) was detected in hemolymph, followed by digestive glands and kidneys (1 014 and 1 015 OTUs), and the gonad had the lowest (only 553 OTUs). Although the number of OTU in hemolymph was the highest, there was only 9 unique OTUs in hemolymph. The kidney had a maximum of 172 unique OTUs, followed by digestive glands (144 unique OTUs). Compositional distribution showed that Proteobacteria, Bacteroidetes and Verrucomicrobia were the main phyla in all tissues. The Bray-Curtis distance results indicated that the bacterial composition of hemolymph, digestive gland, kidney and foot were clustered and the bacterial community from gills, gonads and mantle had higher similarity. Analysis of alpha diversity indicated that the microbiota in hemolymph, digestive glands and kidneys were more diverse than those in other tissues. The variation of indigenous microbiome was attached to different tissues of M. coruscus. Overall, our results will help improve the knowledge of mussel-associated microbial community, and provide a better understanding for revealing the interaction between the mussel and its host-associated microbiota.