Abstract: In the presented study actual problems of the anaerobic microflora impact studying are considered. To conduct the experiment among, weaned pig the animals with clinical signs of dysentery were selected. To establish the histological and ultrastructural changes in the large intestine, the material was obtained from the compulsory slaughtered animals. The histological and ultrastructural study of the mucous membrane of the large intestine in animals with swine dysentery revealed catarrhal hemorrhagic inflammation with focal necrosis of the epithelium and edema of the lamina. It was found that microbiocenosis violation occurs in all parts of the colon in the form of lower levels of normal flora and infestation in the lamina propria. New data allow us to establish pathogenic interrelation between Br. hyodysenteriae and anaerobia which should be taken into account when conducting differential diagnostics and improving measures to combat swine dysentery.