In Japan, under the high growth of economy started in the end of 1950s, remarkable changes of the agricultural structure occurred and economically valuable crops, especially vegetables, flowers and fruits were started to grow under especially intensive managements. As a result, monoculture injuries mainly caused by soilborne diseases became revealed. The control of soilborne diseases of crops is an urgent problem and many researchers are now seeking methods alleviating the damage by the implementation of biological control. As for the biological control methods using antagonistic microorganisms, two ways have been proposed. One is to multiply and activate functionally the microbial community existing in soil and another is to inoculate a specific beneficial microorganism directly into soil for the purpose of suppressing the disease occurrence. The whole entity of the microbial community acts as a functional consortium. Recently, attentions are being paid for understanding the variable functions of soil microbial community and for managing the community towards the specified direction suppressing soil-borne diseases. This is mainly due to the gene technology developed in the recent years in which soil microbial community could be studied using directly extracted DNA from soil. The technology is independent of the conventional culture-based method and could elucidate the relationship between the microbial community and the inhibitory factors for plant production such as monoculture injuries and soil-borne diseases. However, to find out the realistic methods for enhancing the microbial antagonism and utilizing their functions for disease control is still kept in the researcher's dream. So far many efficient biological control agents have been found from the research of utilizing specific antagonistic microorganisms. Some were even successful to be commercialized as microbial fungicides. Plant-associated microbes give physiological and environmental advantages to their host plants. Nowadays, in Japan, biological control using endophytic fungi, actinomycetes and bacteria, and their mechanisms are extensively studied. When we move ahead with the "Integrated Farm System", the significance of biological control is further compounded. The research utilizing specific antagonistic microorganisms follows the exploitation of the microbial fungicides, which could be used at actual agricultural production sites. Such microbial fungicides, however, are restricted to the use inside a closed system. It is necessary to compile many successful examples of biological control not only in greenhouses but also in fields in order to receive much recognition as a general technology of disease suppression by the agricultural producers.