Abstract:The infection of Helicobacter pylori is increasingly drawing the world’s attention, and the radical treatment is the main measure taken by most countries aiming to reduce the rate of infection and subsequent health problems such as peptic ulcer, gastritis and gastric cancer. However, with the increase of drug resistance, especially the increase of macrolide drug resistance, the standard triple therapy is losing its power in controlling the bacteria and new therapies are in urgent need. But most of the new therapies use a longer course, a larger dose and a wider range of antimicrobial agents, and thus can bring severe influences on the structure and quantity of the gut microflora, which may result in severe side effects. Moreover, the deteriorating situation of the antimicrobial resistance will be exacerbated. This review summarized researches in the recent 20 years focusing on the effects that the eradication therapy may bring to the gut microflora. We also summarized some new experimental therapies, thus try to draw a clear profile of our current situation and give some clues for the treatment of Helicobacter pylori.