Background: It is estimated that more than 80% of cases of human infections are related to biofilm formation by invasive bacteria. So, in this study, we considered the activity of cellobiose dehydrogenase enzyme (CDH) isolated from Aspergillus niger, as an antibiofilm agent, on biofilm of clinical Staphylococcus epidermidis and Pseudomonas aeruginosa isolates. Methods: In this study, five standard strains of Aspergillus niger were purchased for CDH production. Of the 42 isolated bacterial strains, 24 strains were Staphylococcus epidermidis and 18 strains were Pseudomonas aeruginosa. Zymogram method was used for screening of CDH. The CDH activity was measured by monitoring the decrease in absorbance of 2, 6-dichlorophenolindophenol (DCPIP) spectrophotometrically. After cultivation and production of bacterial biofilms, 7 concentrations of the cellobiose prepared and CDH enzyme with a final concentration of 364 U/mL were considered on bacterial biofilms by microbroth dilution method. Results: Out of five standard strains of Aspergillus niger, only 1 strain have the highest production of CDH. The most effective dilution of cellobiose on growth inhibition of Staphylococcus epidermidis and Pseudomonas aeruginosa in liquid cultures as a function of cellobiose concentration in the presence of cellobiose dehydrogenase was in 12.5 µg/mL. Conclusions: Based on the results of this study, it can be concluded that the CDH enzyme had a high potential for use as an antimicrobial agent. As shown, this enzyme had a high potential for eliminating bacterial biofilms. So, these results may provide a basis for alternative therapies for the treatment of infections related to clinical biofilm producing bacteria.