Myristica fragrans Houtt is mostly cultivated for spices in Penang Island, Malaysia. The ethyl acetate and ethanol extracts of flesh, mace and seed of Myristica fragrans was evaluated the bactericidal potential against three Gram-positive cariogenic bacteria (Streptococcus mutans ATCC 25175, Streptococcus mitis ATCC 6249, and Streptococcus salivarius ATCC 13419) and three Gram-negative periodontopathic bacteria (Aggregatibacter actinomycetemcomitans ATCC 29522, Porphyromonas gingivalis ATCC 33277, and Fusobacterium nucleatum ATCC 25586). Antibacterial activities of the extracts was determined by twofold serial microdilution, with minimum inhibitory concentrations (MIC) ranging from 1.25 to 640 mg/mL and 0.075 to 40 mg/mL. The minimum bactericidal concentration (MBC) was obtained by subculturing method. Among all extracts tested, ethyl acetate extract of flesh has the highest significant inhibitory effects against Gram-positive and Gram-negative bacteria with mean MIC value ranging from 0.625 to 1.25 ± 0.00 (SD) mg/mL; P = 0.017) and highest bactericidal effects at mean MBC value ranging from 0.625 mg/mL to 20 ± 0.00 (SD) mg/mL. While for seed and mace of Myristica fragrans, their ethanol extracts exhibited good antibacterial activity against both groups of test pathogens compared to its ethyl acetate extracts. All of the extracts of Myristica fragrans did not show any antibacterial activities against Fusobacterium nucleatum ATCC 25586. Thus, our study showed the potential effect of ethyl acetate and ethanol extracts from flesh, seed and mace of Myristica fragrans to be new natural agent that can be incorporated in oral care products.