The studies that were conducted for 82 patients with ulcer established that 22 genera of microorganisms including H. pylori in a combination from 2 up to 8 various microbial cultures can be secured from the biopsy of the mucous coat of the pre-ulcer zone at the acute phase of recurrence. They have high enzymatic and cytotoxic activity. This draws together microbiological characteristics of the ulcer defect with parameters of the infected wound and corresponds to dysbacteriosis of the third degree. The data obtained form the basis for considering that the exacerbation of ulcer is accompanied by expressed dysbiotic shifts depending on the recurrence phase. It is necessary for taking this into account in the development of methods of adequate therapy for the disease aimed at the suppression of the excess growth of mucous microflora and restoration of normal microbiocenosis in the gastroduodenal zone.