Abstract: There are a variety of endophytic microorganisms in the roots and leaves of tea plants, which will lead to the pollution during the tissue culture, affecting the growth of cultures and the process of genetically modified breeding. In the present study, endophytic microorganisms in the leaves from three tea cultivars in the same field were isolated. The microscopic morphology observation showed that the dominant endophytic microorganisms were different in three tea cultivars. It is Bacillus in Camellia sinensis cv Huangjinya, Alternaria in C. sinensis cv Longjing 43 and Colletotrichum in C. sinensis cv Jiaming 1, respectively. Therefore, different anti-pollution measures should be taken in tea plant tissue culture.