Objective: Alterations in the gut microbiota (dysbiosis) have been linked to the development of type 2 diabetes mellitus (T2DM). Dysbiosis disrupts the function of tight junction proteins, which allows translocation of lipopolysaccharides into the blood stream. This, in turn, causes onset and progression of inflammation that leads to metabolic endotoxaemia. This systematic review highlights the latest evidence of differential composition of gut microbiota between T2DM patients and healthy individuals that was obtained through high-throughput molecular approaches. Methods: Literature search was conducted using three electronic databases with restriction to English language. Search terms included diabetes, gut microbiota, faecal microbiota and sequencing. Independent selection of studies and quality assessment were performed by two authors. Results: A total of 10 case-control studies, which involved T2DM patients and healthy individuals, fulfilled the inclusion criteria. It was found that bacteria associated with T2DM could be influenced by dietary consumption, ethnicity, age, method used to analyse gut microbiota composition and medication amongst others. By combining the composition of microbiota across ten studies, T2DM patients were presented with marked increase in opportunistic pathogens within the phylum of Firmicutes but a decrease in short chain fatty acid (SCFA)-producing bacteria. There was no difference between T2DM patients and healthy individuals in terms of Bacteroidetes abundance. Six studies found that lactobacilli predominated the gut of T2DM patients. Conclusion: A remarkable shift in the gut microbiota composition was observed in T2DM when compared to controls in all studies. The current systematic review had identified gaps which included heterogeneity, the lack of in-depth analysis of gut microbiota compositions and varying methods of assessment that need to be addressed in future studies.