Natural drugs usage as alternative treatment has been increased in decades. This is due to the ‘back to nature’ life style of people and the side effect of natural drugs are relatively low. The prices of these natural drugs are cheaper as well. Papaya seed is one of the natural product with antimicrobial effect. The objectives of this research were to determine Minimum Inhibitory Concentration (MIC) of papaya seed ethanol extract to inhibit the growth of Candida albicans and Vibrio cholera and to analyze its active compounds. This research was performed using experimental design laboratory. The ethanol extract of papaya seed was obtained by maceration. The antimicrobial assay of papaya seed ethanol extract was performed using agar plate diffusion. The MIC determination of papaya seed ethanol extract was performed by 20, 15, 10, 5 and 1% concentration. The MIC of papaya seed ethanol extract against Candida albicans and Vibrio cholerae were in 5% concentration (diameter of inhibition zone=0.75 mm) and 15% (diameter of inhibition zone = 14.75 mm), respectively. The phytochemical assay of papaya seed ethanol extract showed there were alkaloids, flavonoids, steroids, polyphenols, tannins and saponins. It means that papaya seed ethanol extract has a good potential as antimicrobial therapy agent.