In this article the method of green fluorescence protein and antibiotics were adopted to mark the specific functional microbes for researching the effect of biologic organic fertilizer FBOF1 and FBOF2 on flue-cured tobacco growth and its defensive-related enzymes,meanwhile,depending on the pot experiment the colonization of functional microbes in the rhizosphere was researched,and the effect of biological organic fertilizer on flue-cured tobacco growth and the defensive-related enzymes such as polyphenol oxidase,peroxidase,phenylalanine ammonialyase and lipoxygenase was also researched.The results indicated that utilizing biological organic fertilizer could promote tobacco growth and the biomass indexes as plant height,leaf area,fresh weight and dry weight increased.The leaf area of 30th day improved 26.20% and 30.87% compared with the control,and the difference is obvious,and the fresh weight increased 30.6% and 36.72%,while the dry weight is 47.93% and 23.97% more respectively.The soil nutrient status was also improved by applying the biological organic fertilizer,and the organic matter,the alkaline N,available K and total P increased.The results also demonstrated that the functional microbes in the biological organic fertilizer can colonize successfully in the rhizosphere,and can inhibit the reproduction of deleterious pathogenic microorganism in some degree.In addition,the activity of defensive-related enzymes such as PPO,LOX and PAL etc.were improved after utilizing biological organic fertilizer,in which the activity of PPO in 7th day increased 38.1% and 35 8%,while 19.6% and 17.5% for the LOX,and the same level 2⁴.5% for PAL,and the increase of enzymes activity leads to the enhanced disease-resistance ability for the plant.