Objective Changes in microbiota composition in the distal esophagus may be associated with the pathogenesis of gastroesophageal reflux disease. We aimed to compare the composition of distal esophageal microbiota between Chinese patients with reflux esophagitis (RE) and healthy volunteers using metagenomic high-throughput DNA sequencing and bioinformatic analyses. Methods Healthy volunteers (controls) and patients with reflux esophagitis (RE) were enrolled. Distal esophageal (2 cm above the gastroesophageal junction) biopsy specimens were obtained under endoscopy. Microbial DNA was extracted from the specimens, followed by 16S rDNA gene amplification and Illumina sequencing. Bioinformatic tools were applied to dissect the community structure. Results No dramatic differences in microbiota were found in RE patients compared with the controls. At the phylum level, only Bacteroidetes differed between the groups, being less abundant in the RE group. The overall number and diversity of species tended to be lower in RE patients, but there were no significant differences between the groups. Three genera, Prevotella, Helicobacter, and Moraxella, were obviously depleted in RE patients, as revealed by linear discriminant analysis. Conclusions The composition of distal esophageal microbiota in Chinese patients with RE showed moderate changes compared with healthy controls. To what extent these changes are associated with the pathogenesis of RE needs further investigation.