Functional dyspepsia (FD), a widespread and debilitating digestive disease, is thought to originate from disrupted gut-brain communication. The cause of FD is not completely understood, but recent evidence suggests it could be due to multiple factors and can vary among different patient groups. Factors like gut motility changes, increased sensitivity to pain in the gut, ongoing low-level inflammation, and increased gut permeability have all been linked to the development of FD. Additionally, changes in the gut microbiome have been suggested to play a significant role in the disease. The gut microbiota in the duodenum could either be a cause or a result of the immune and nervous system issues seen in FD, but the ways in which the gut flora in the small intestine affects gut function, digestive metabolites and symptoms are not yet clear, more studies being needed in order to completely assess the relationship between gastrointestinal microbiota and development and progression of FD. This review summarizes the available research on the relationship between FD and the microbiota and examines the various treatments, including probiotics, that have been shown to relieve symptoms. Finally, suggestions for improving diagnosis and treatment for those with FD are presented.