The microorganisms that are formed in biofilm cause about 60% of chronic and recurrent diseases, and as a consequence, traditional etiotropic antibacterial therapy is ineffective. Chronic anal fissures are also a disease which is caused by biofilm forms of bacteria, has a chronic course and is difficult to treat. The sensitivity of planktonic and biofilm forms of bacteria isolated from chronic anal fissures to antibacterial drugs was determined and the method of degradation of biofilm by electrophoresis for the effective treatment of fissures was developed. It was found that the most effective antibiotics against planktonic forms of bacteria were cephalosporins III and IV generations: cefеpime, cefoperazone and ceftazidime. Exceptionally, only bacteria of the genus Enterococcus, which were sensitive to ceftazidime, were found to be 38.9%. The sensitivity of the bacteria to Furamag was from 60.0% to 100.0%, and only P. aeruginosa exhibited resistance in 100.0% of the studied cultures. The number of sensitive to gatifloxacin strains of P. aeruginosa and Enterobacter spp. was 71.4%, all other isolated bacteria were sensitive to this preparation from 77.8% to 100.0%. Among the five studied antiseptics (chlorhexidine, decasan, octinisept, povidone iodine, dioxidine), the greatest antimicrobial activity was found in dioxidine and betadine (povidone iodine) solutions, the sensitivity of the microflora was from 60.0% to 100.0%. We found that the most protected biofilm matrix was P. aeruginosa and Enterococcus spp. We found that the antibiotic which had the best effect on cells in biofilm was fluoroquinoione gatifloxacin. After its influence on the biofilm P. aeruginosa and Enterococcus spp., the number of living cells didn’t exceed lg 1.5 ± 0.02 CFU/cm2 in the area of the biofilm, and S. aureus and E. coli cells were completely inactivated. After the influence of other antibiotics, the number of microbial cells that survived in the biofilm did not exceed lg 2.9 ± 1.6 CFU/cm2 of the area. It was found that after the action of dioxin, the amount of viable microbial cells was up to lg 2.9 ± 1.7 CFU/cm2 of biofilm area. Antiseptics: octine septum, ranopost, decaSan and chlorhexidine exhibited less strong bactericidal action on cells in biofilms, and the number of bacteria that survived after their action ranged from 2.9 ± 1.8 to lg 3.7 ± 2.1 CFU/cm2 of biofilm area. We propose using solution "Dioxysol-Darnitsa" (active substance dioxidine) for local treatment of patients with chronic anal fissures for intracutaneous electrophoresis of the fissure. We established that under the influence of electrophoresis at a current of 0.05–0.10 mA/cm2 of the area of the biofilm with dioxidine, bacteria were not isolated. This indicates on the destruction of the matrix and the effective contact of dioxidine with microbial cells and the manifestation of bactericidal action. Consequently, laboratory microbiological studies indicate that the use of electrophoresis with dioxysole in the treatment of chronic anal fissures is promising.