The mouth is a favorable habitat for a great variety of bacteria. Microbial composition of dental plaque is the usual cause of various oral diseases in humans, including dental caries, periodontal disease and halitosis. In general, oral antibacterial agents such as antibiotics are commonly used to treat oral bacterial infection. Traditional periodontal surgery is painful and time-consuming. In addition, bacterial resistance and toxicity of antibiotics have become a global pandemic and unavoidable. Recently, vaccines for dental caries and periodontal disease have been developed and applied. Moreover, the use of photodynamic therapy has become an alternative to antibiotic drugs. The purpose of this article is to highlight the advantages of vaccine therapy and photodynamic therapy for oral microbial-related diseases compared to treatments with antimicrobial agents and traditional periodontal surgery.