Esophagus, as the pipe connecting oral cavity and stomach, has unique anatomical structure and physiological functions. The related diseases including esophageal cancer and precancerous lesions are the ones of major public health problems in China. The pathogenesis of esophageal diseases is still not clear. The exploration of correlation between the changes of esophageal microbiota and esophageal diseases becomes a new breakthrough in the study of etiology. Previous studies have found enrichment of gram-positive bacteria in the normal esophagus, while a decrease in diversity of bacteria and a dominant gram-negative anaerobe in diseased esophagus. Although much progress has been made in the study of esophageal microbiota, the standard method of how to accurately and noninvasively collect esophageal microbiota is still lack, which is an important part of the esophageal microbial research.