Patients with gastric cancer harbor distinct microbiota in the stomach. It features with lowered biodiversity, discrete structure, and varied composition. Some bacteria from gastric microbiota are potentially carcinogenic as they are enriched or depleted in gastric cancer. Distinct profile of microbial community in gastric cancer is possibly resulted from altered caused by pathophysiological and environmental factors. H. pylori is a carcinogen colonizing the human stomach. Although persisting for decades, it rarely causes compositional alteration of microbiota. Secretion of acid decreases gradually during the carcinogenic process. Increased pH results in overgrowth of bacteria in gastric fluid. The abundance of a particular taxon, but not the profile of microbiota, is altered in proton pump inhibitor users. Compositions of microbiota vary substantially between individuals, which may account for differential cancer risk. It has been demonstrated that genetic variations contribute to inter-individual variations in gut microbiota. However, their influence on the composition of gastric microbiota requires further exploration. Currently, it appears disrupted homeostasis and inter-individual variations of gastric microbiota are involved in cancer development. Clarifying factors responsible for these changes would reveal how microbiota induces carcinogenesis, benefiting the prevention of gastric cancer.