This work compared the inhibition effect of the commercially available mouthwash Corsodyl, containing 0.1% chlorhexidine digluconate, and photodynamic inactivation (PDI) employing methylene blue (MB) with irradiation from a red laser on 24-h biofilms formed by Streptococcus mutans strains on hydroxyapatite surfaces. The cytotoxicity of Corsodyl and MB was evaluated by Galleria mellonella surviving assay. The viability of biofilm cells after exposure to mouthwash and PDI was determined by counting colony-forming units. The inhibitory effect of antimicrobial agents was confirmed by confocal scanning laser microscopy. MB did not exhibit a cytotoxic effect on larval survival. Non-diluted Corsodyl slightly decreased the survival of larvae. Using our PDI parameters achieved better inhibition than with non-PDI, proving a significant effect on the eradication of S. mutans biofilms and therefore could be an appropriate supplement for the eradication of dental caries.