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The bacteria of shellfish bioaccumulate mainly in the gill and digestive gland tissues, which can affect shellfish health status and disease susceptibility under stressful conditions or environmental effects. Ruditapes philippinarum is a filter-feeding shellfish with both ecological and economic significance, and it is classified as a Mollusca (phylum), Bivalvia (class), Veneridae (family), and Ruditapes (genus). In this study, 16S high-throughput sequencing was used to explore the microbiomics of digestive glands and gills of R. philippinarum under temporary rearing without feeding (including the purification process) in different water environments (natural vs. artificial seawater) from 0–7 days. The results revealed that the digestive glands and gills of R. philippinarum had their own unique bacterial community structures. Tissue microorganisms under the overlap of different water environments and starvation factors showed different dynamic effects within 0–7 days. The sand spitting and purification steps (posttransport rehydration stage of 24 hours) effectively reduced microorganism abundance. There were different biomarkers in the prerearing and postrearing periods, and R. philippinarum may be more susceptible to the enrichment of opportunistic pathogenic bacteria during the postrearing period in artificial seawater. [ABSTRACT FROM AUTHOR]