Little is known about the link between gastric microbiota and the epidemiology of gastric cancer. In order to determine the epidemiologic and clinical relevance of gastric microbiota, we used 16 S ribosomal RNA gene sequencing analysis to characterize the composition and structure of the gastric microbial community of 80 paired samples (non-malignant and matched tumor tissues) from gastric cardia adenocarcinoma (GCA) patients in Shanxi, China. We also used PICRUSt to predict microbial functional profiles. Compared to patients without family history of upper gastrointestinal (UGI) cancer in the non-malignant gastric tissue microbiota, patients with family history of UGI cancer had higherHelicobacter pylori(Hp)relative abundance (median: 0.83vs. 0.38,p = 0.01) and lower alpha diversity (median observed species: 51vs. 85,p = 0.01). Patients with higher (vs. lower) tumor grade had higherHprelative abundance (0.73vs. 0.18,p = 0.03), lower alpha diversity (observed species, 66vs. 89,p = 0.01), altered beta diversity (weighted UniFrac,p = 0.002) and significant alterations in relative abundance of five KEGG functional modules in non-malignant gastric tissue microbiota. Patients without metastases had higher relative abundance ofLactobacillalesthan patients with metastases (0.05vs. 0.01,p = 0.04) in non-malignant gastric tissue microbiota. These associations were observed in non-malignant tissues but not in tumor tissues. In conclusion, this study showed a link of gastric microbiota to a major gastric cancer risk factor and clinical features in GCA patients from Shanxi, China. Studies with both healthy controls and gastric cardia and noncardia cancer cases across different populations are needed to further examine the association between gastric cancer and the microbiota.