Selective Serotonin Reuptake Inhibitor (SSRI) therapy is common among perinatal populations for the treatment of mood disorders. Medications can affect diversity and composition of the gut microbiome, which plays a key role in modulating health. While previous studies have examined the effects of antidepressant exposure on the maternal gut microbiome, whether SSRI exposure affects the offspring gut microbiome is unknown. We investigated the effects of maternal fluoxetine exposure on the gut microbiome of maternal and offspring mice during pregnancy and lactation (embryonic day 10-lactation day 21; E10-L21). Stool samples collected on E17, L11, L15, and L21 were examined using 16S rRNA sequencing. Our results suggest that maternal fluoxetine exposure may result in decreased alpha diversity of the offspring gut microbiome in early life. Furthermore, we observed several genera-specific differences in the gut microbiome based on treatment, specifically of Turicibacter, Parasutterella, and Romboutsia. These findings support our understanding of gut health, as dysbiotic development of the gut microbiome has been associated with local and systemic health problems including gastrointestinal morbidities and interrupted growth patterns in infants. Future research should pursue study in human populations and those at high risk for gut microbial dysbiosis and intestinal injury.