In this study, microorganisms were isolated from the soil in Ohda city (Shimane prefecture, Japan) and screened for their inhibitory activity against Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae. Ninety-six microbial isolates were obtained from the soil samples. Three isolates (S1004, S1011, and S2001) inhibited the growth of X. oryzae pv. oryzae compared to the control. Mycelial growth of M. oryzae was inhibited by the isolate S2001, but not by the isolates S1004 and S1011. Furthermore, conidial germination in M. oryzae was inhibited by the culture filtrate of isolate S2001. This study showed that the isolate S2001 might be able to control the diseases caused by M. oryzae and X. oryzae pv. oryzae.