Bivalves filter and accumulate large numbers of microorganisms present in the harvesting water. A complete understanding of the balance between Anodonta cygnea and the microbiota present in their surrounding environment remains incomplete. Therefore, the aim of this study was to quantify and identify the indigenous bacteria in the biological fluids of A. cygnea collected from Mira Lagoon in northern Portugal. The results showed Vibrio metschnikovii and Aeromonas sobria as the dominant groups. The median for total bacteria from mucus was 3.1 × 10(3) CFU g(-1), whereas the range in means from fluids was 1.5 × 10(2) to 6.5 × 10(2) CFU ml(-1). During the experimental work, Escherichia coli and enterococci were not detected in healthy A. cygnea. However, the periodic detection of E. coli and enterococci in Mira lagoon revealed its presence in the water. Our observations suggest that A. cygnea has the ability to filter and eliminate E. coli, present in the surrounding environment, through an active phagocytic process conducted by hemolymph circulating cells, the hemocytes.