Gut microbiota impacts host homeostasis and diseases. Chronic plus binge ethanol consumption has been linked to increased injuries than chronic or binge ethanol intake alone. We hypothesized that distinct shapes in gut microbiota composition are induced by chronic, binge, and the association of these treatments, thereby affecting host functions and contributing to sex-based differences in alcohol use disorders. Male and female C57BL/6J mice were submitted to chronic, binge, or chronic plus binge ethanol feeding. DNA was extracted from fecal microbiota, followed by analysis of the V3-V4 region of the 16S rRNA gene and sequencing on an Illumina platform. Gut microbiome analysis was performed using QIIME v2022.2.0. Functional profiling of the gut microbiome was performed using PICRUSt2. Ethanol differentially affected the gut microbiota of female and male mice. Decreased α diversity was observed in male and female mice from the chronic plus binge and chronic groups, respectively. The genera