Changes in gut microbiota have shown that it plays an important role in animal health and metabolic diseases. The intestinal microbiota is a complex structure that functions as an organ system with the presence of trillions of microorganisms. In this study, changes in the intestinal microbiota of Wistar rats with high fluorine were evaluated. Water containing 100 ppm NaF was given to 14 male Wistar albino rats as drinking water for 12 weeks. Fluorine is known to be an inducer of protein oxidation, lipid peroxidation, modulation of intracellular redox homeostasis, and oxidative stress. In this study, it was determined that the level of MDA (molandialdehyde), one of the oxidative stress parameters, increased significantly in the intestinal tissue after fluorine intoxication. The decrease in CAT (catalase) and SOD (superoxide dismutase) enzyme activities was found to be statistically significant. Intestinal tissues were taken under aseptic conditions and microorganisms found in flora were replicated by V3-V4 16S rRNA gene-specific primers. As a result of the sequence analysis, a statistical comparison of the control group and the fluorine applied group was made. The study we have done showed that there was a significant difference in species diversity in the intestinal microbiota of mice treated with fluorine. As a result, the composition of the intestinal microflora, especially Lactobacillus species, was significantly changed in rats with high fluorine.