The total numbers of actinomycetes, fungi and bacteria were lower in the single crop system of soybean or maize at Sakha and Itay El-Baroud Agriculture Research Stations. The most antagonisticmicroorganisms were selected and identified as Trichderma viride;  Bacillus subtilis and Streptomyces sp. High numbers of total counted microorganisms were found in the system pattern (2 rows soybean: 2 rows maize) followed by (2 rows soybean: one row free, one row maize (2:1). The total counts of fungi and bacteria were higher under sole cropping condition in maize (soybean 0:4 maize), than sole cropping of soybean (soybean4:0 maize). However, actinomycetes showed some differences than this trend. Generally, the numbers were increased by time from seedling stage to flowering stage, and then decreased or become almost stable at mature stage. The antagonism between the pathogenic fungi and each of bioagents indicated that B. subtilis showed the highest reduction in linear growth followed by T. viride while, Streptomyces sp. showed the lowest reduction. Bacillus subtilis was the most effective bioagent in the reduction of pre-and post-emergence damping-off and increased survival plants percentages followed by T. viride, while the Streptomyces sp. was the least effective. Effect of soybean-maize intercropping system on soybean damping-off disease under field experiment indicated that the highest incidence was observed in 3:1 soybean: maize pattern while, 2:1 was the lowest disease incidence compared with other intercropping systems. The mono crop system of each soybean alone or maize alone resulted in the highest yield (kg/plot) in the two locations. While the yield of both soybean and maize in the four systems of intercropping i.e. (3:1, 2:2, 2:1 and 1:1) was higher as Land Equivalent Ratio (LER) in the system of 2:1compared with 3:1 system.