UNLABELLED: Gastric disorders have been associated with changes in the abundance and composition of microbiota, which typically coexist in symbiosis within the stomach. There is a scarcity of data regarding the presence of gastric mucosa-associated dysbiosis in functional dyspepsia. The present study aimed to characterize the taxonomy and diversities of the microbiota in the gastric mucosa of patients with functional dyspepsia. The study was conducted on a total of 50 paired antral and body gastric biopsies collected from the dyspepsia group ( = 15) and control group ( = 10). Microbial DNA was extracted from all gastric biopsies, followed by 16 S rRNA gene next-generation sequencing (NGS) using the Miseq Illumina platform. Firmicutes, Proteobacteria, and Bacteroides were the most predominant phyla in both groups, with a significant overrepresentation of Proteobacteria in the dyspepsia group ( value = 0.004). The genera , , and were the most prevalent in both groups. The species of and were significantly more abundant in the dyspepsia group. The species of The LEfSe analysis revealed that , , , , and were the most highly abundant and discriminating taxa in the gastric biopsies of the dyspepsia group compared to the control group. The microbial alpha diversity was significantly higher among gastric biopsies of dyspepsia than controls ( = 0.031). The beta diversity showed microbial dissimilarity between samples of dyspepsia and the control group. The 16 S rRNA gene NGS used in the present study demonstrated significant alteration in composition and diversities of gastric mucosa-associated microbiota among cases of functional dyspepsia compared to the controls. It is advisable to utilize advanced innovative technologies to gain a deeper understanding of the underlying pathophysiology of disrupted microbiota in gastric disorders. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04095-0.