BACKGROUND: Some microorganisms extant in nature have ability to suppress various plant pathogens, and also can promote plant growth. Thus microorganisms are such great source of antimicrobial agents to develop antagonistic microorganism production and eco-friendly crop management. We isolated the microorganisms in various eco-friendly formulations. The suppressive abilities against plant pathogens have been characterized in vitro level. METHODS AND RESULTS: The indigenous microorganisms have been isolated from Cooked rice, Black sugar, Rice Bran, and Red clay using dilution plating method. Population of bacteria and fungi were above 107 in the all formulations. We isolated and pure cultured the microorganisms based on morphological characteristics. Three major plant pathogens (Fusarium oxysporum, Rhizoctonia solani, Phytophthora capsici) have been used to select antagonistic microorganisms. Total 20 bacteria and 9 fungi showed the pathogen growth suppression ability in vitro condition. The selected microorganisms were identified by ITS sequence similarity. CONCLUSION: All tested eco-friendly formulations contained high-density of the microorganisms. Among the isolated microorganisms, Bacillus spp. and Streptomyces spp. showed the most effective antifungal activity against the plant pathogens such as F. oxysporum, R. solani, and P. capsici. Among the selected fungi Trichoderma sp. demonstrated antifungal activity. Our results suggest that the currently adapted eco-friendly formulations might useful for sustain agricultural system.