Peanut - sesame intercropping was studied under (2:2) and (3:1) pattern with 45, 60 and 75 kg nitrogen/feddan to determine their effect on the total count of bacteria and fungi as well as the incidence of root-rot and wilt diseases (dead plants) and yield components of both crops in Ismailia Agricultural Research Station during 2010 and 2011 growing seasons. Results indicated that intercropping pattern (2:2) increased the total count of bacteria and fungi isolated from the soil than that in (3:1) pattern. Also, it increased the total count of fungi responsible for root-rot and/or wilt diseases (dead plants) of both crops. Increasing nitrogen fertilizer rate from 45 to 75 kg nitrogen/feddan increased the total count of fungi and decreased the total count of bacteria. On the other hand, the increase of nitrogen fertilizer rate resulted in increasing the percentages of dead plants of both crops under both intercropping system during the two growing seasons. The values of land equivalent rate (LER) of (2:2) pattern exceeded than (3:1) pattern. The highest LER was obtained with (2:2) pattern when fertilized with the highest nitrogen fertilizer rate (75 kg N/fed.). Results also indicated that the yield of sesame in (2:2) pattern was the superior and the opposite was recorded for peanut in case of (3:1) pattern. In addition, increasing the dose of nitrogen fertilizer resulted in increasing the values of crop parameters than the other two rates whatever the pattern of the intercropping.