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Thallium (Tl) is a highly toxic trace metal widely distributed in water environments, which may threaten the water quality and aquatic organisms at excessive levels due to increased anthropogenic activities. This study investigated the changes in microbial communities of intestines and organs of zebrafish. The toxic response assessments include intestinal microbiota composition and the histopathology of zebrafish’s gill and liver tissues under exposure of Tl at environmental-relevant levels. The results support that the intestinal microbial community of zebrafish greatly changed under a relatively high Tl concentration (1000 ng/L). A significant increase of pathogenic intestinal bacteria such as Mycobaterium in the intestine of zebrafish exposed at Tl levels over 500 ng/L was found. Additionally, the gill and liver tissues displayed different degrees of damage under Tl exposure, which possibly leads to mating behavior changes and death of zebrafish. The results indicate that low doses of Tl in the aquatic environment induce high toxicity on zebrafish and may pose pathological threats to the gill and liver of zebrafish. In addition, Tl exposure gives rise to increasing abundance of pathogenic intestinal bacteria and changes the community structure of intestinal microorganisms.