In this study, we compared disease incidence rate and phyllosphere microbial community between drought resistance transgenic rice (Agb0103) and non-transgenic Ilmi (NGM) during 2011-2014 to examine an environmental risk assessment of drought resistance transgenic rice (Agb0103). As the results, major diseases such as sheath blight, brown spot, leaf blast and false smut were occurred, however, there were no significant disease incidence rate between Agb0103 and NGM. As the results of counting bacterial and fungal viable cell, the colonies were increased or decreased which affected by environmental conditions, however there were no differences between Agb0103 and NGM. Also unweighted pair-group method with arithmetic averaging (UPGMA) analysis based on polymerase chain reaction with denaturing gel electrophoresis (PCR-DGGE) revealed that DGGE band pattern of bacterial and fungal communities were clustered by each month and there were no differences between Agb0103 and NGM. Furthermore, isolated casual agents causing sheath blight and brown spot were collected from Agb0103 and NGM, and they revealed that each of pathogens were no differences in morphology and pathogenicity. Therefore, our results suggested that Agb0103 showed no differences in disease incidence rate, characteristic of pathogens and phyllosphere community with NGM. In this way, it can be assumed that transgenic rice Agb0103 could not influence phyllosphere microorganism community and environmental conditions.