Early blight and Fusarium wilt are from prevalent diseases in potato and tomato fields in East Azerbaijan province and cause a great damage to crop yield annually. In this research, biological control of these diseases was studied by application of Bacillus methylotrophicus in vivo and in vitro conditions. In laboratory experiments, the suspension of antagonistic bacterial cells (108 cfu ml-1) was sprayed on 30 days old plants two times in 5 days intervals. For biological control of tomato Fusarium wilt, the bacterial suspension was applied trough root system of 30 days old plants. Treated plants were inoculated with their related pathogens after 48 hours. According to the results in laboratory conditions, B. methylotrophicus was able to inhibit the mycelial growth of pathogens in dual culture test as 75, 80 and 78% in early blight of potato, early blight of tomato and Fusarium wilt of tomato respectively and the inhibition zone around of fungi colony in three mentioned diseases was measured as 1.2, 1.33 and 0.82 centimetre respectively. In the test of volatile metabolites, antagonistic bacterium was not able to affect the mycelial growth and it seems that antagonistic bacterium causes control of pathogens by producing non-volatile metabolites and different antibiotics. In glasshouse conditions, antagonistic bacterium reduced the disease severity of early blight of potato, early blight of tomato and Fusarium wilt of tomato as 35, 40 and 74% respectively. Due to the positive effect of this bacterium especially on control of tomato Fusarium wilt, it is recommended that tomato seedlings treat with bacteria before transplanting in main plots and plants spray with bacterial suspension at susceptible stages of tomato and potato plants to early blight disease.