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Periodontitis and tooth decay are common dental diseases. There are some bacterial risk factors such as Streptococcus mutans, Aggregatibacter actinomycetemcomitans and Candida albicans complications, tubers of Cyperus rotundus was used to determine the antimicrobial effect of fungi. Considering the increasing resistance of bacteria and fungi to antibiotics and their alcoholic and aqueous extracts and essential oil on Streptococcus mutans, Aggregatibacter actinomycetemcomitans and Candida albicans, as well as an examination cytotoxicity on gingival fibroblast cells. Alcoholic and aqueous extracts and essential oil prepared from tubers of Cyperus rotundus. After bacterial and fungal cultures, the inhibition zone, Minimum inhibitory concentrations (MIC), and Minimum Bactericidal Concentration (MBC), were studied. Cytotoxicity was also evaluated using the Methyl tetrazolium test (MTT).The results showed that Cyperus rotundus alcoholic extract had the greatest effect on inhibition of growth and death of Streptococcus mutans, Aggregatibacter actinomycetemcomitans. According to the present study, Cyperus rotundus extract can be considered as a suitable candidate for the treatment and prevention of periodontitis and tooth decay.