In order to understand the distribution character and the relationship of plant diseases with endophytes, studies on the quantity, classification and antagonism of endophytes from seeds, stems and leaves were conducted on four species of high-quality tobaccos. The tobaccos studied were K326, G-80, Hong Hua Da Jing Yuan and Jing Ye Huang. The results showed that the endophytic microorganisms existed widely in tobaccos. Bacteria were the most abundant followed by actinomycetes, then fungi. This reflects microbial distribution in soil. However, endophytes are not equally distributed in each organ. The root and seed contain the most, followed by stem with leaf containing the least. Among different species of tobaccos the distribution of endophytes is also variable. Endophyte distribution in the seed of K326 and Hong Hua Da Jing Yuan is the highest, with Jing Ye Huang next and G-80 containing the least. During the seedling period no obvious distinction was observed among the four species. During gruthduration after transplant Jing Ye Huang contains the least endophytes. Gram-negative bacteria are the most abundant in the all four species of tobacco and the quantity of spore bacteriain seeds is apparently higher than that of whole plants. Through antagonistic experiments of Escherichia coli and Staphylococcus aureus, we isolated five strains from Hong Hua Da Jing Yuan and one each from Jing Ye Huang and K326.The results indicated antagonistic characteristics of the four species is related to the antibacterium to some extent.