Abstract Four fungal chitosan types (CTS) were prepared from Mucor rouxii DSM 1191 and examined for their physico-chemical characteristics. The antimicrobial activity of chitosan types against 11 bacterial strains, including six pathogens, was investigated and the most effective type was chitosan No. 3 which was characterized with the lowest viscosity and molecular weight (3.1 cP and 2.1 × 10 4 Da, respectively), the highest degree of deacetylation (95%) and neutral water solubility. Gram positive bacteria were generally more sensitive to chitosan antimicrobial action than Gram negative strains and this action was notably affected by the environmental growth conditions, i.e. incubation temperature and pH value. The applications of fungal chitosan for the suppression of bacterial pathogens as a natural alternative, reduced risk and biodegradable biocidal agent could be recommended.