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Abstract Objective Streptococcus mutans is one of the principal causative agents of dental caries (tooth decay) found in the oral cavity. Therefore, this study investigates whether selenium nanoparticles (SeNPs) enhance the efficacy of photodynamic therapy (PDT) against both planktonic communities and the one-day-old biofilm of S. mutans. In this study, the planktonic and 24-h biofilm of S. mutans have been prepared in 96-cell microplates. These forms were treated by methylene blue (MB) and SeNPs and then were exposed to light-emitting diode (LED) lighting. Finally, the results have been reported as CFU/ml. Results The outcomes demonstrated that MB-induced PDT and SeNPs significantly reduced the number of planktonic bacteria (P-value < 0.001). The comparison between the treated and untreated groups showed that combining therapy with SeNPs and PDT remarkably decreased colony-forming units of one-day-old S. mutans biofilm (P-value < 0.05). The findings revealed that PDT modified by SeNPs had a high potential to destroy S. mutans biofilm. This combination therapy showed promising results to overcome oral infection in dental science.