The aim of this study was to determine the effect of effective microorganisms (EM) on growth, yield and fruit nutrient contents of two cultivars (‘Muhanjilju’ and ‘Daetong’) of hot pepper. The number of injection of EM cultivated are 6 times from the pepper plant seedlings until harvested in both cultivars. Stem girth was highest in the treatment of Lactobacillus plantarum whereas lowest in no EM control. In ‘Muhanjilju’, the number of branches was highest (79.3) in the treatment of Bacillus subtilis whereas in ‘Daetong’ was highest (119.0) as treated with Lactobacillus plantarum. Yield of the red hot pepper fruits that sum of two varieties was highest in the treatment of Rhodopseudomonas capsulatas (53.1kg FW per 10a). Regardless of EM treatments, average yield was 8% higher in ‘Daetong’ than is ‘Muhanjilju’ (33.8kg vs 31.2kg per 10a). The incidence of antracnose was lowest by the Rhodopseudomonas capsulatas treatment, which led to the highest yield. As for the effect on fruit mineral nutrients, total N and phosphorus concentrations were highest in the treatment of Lactobacillus plantarum and Bacillus subtilis in both varieties, respectively. The highest content of total carotenoids was obtained from the treatment of Lactobacillus plantarum in both varieties.