Most of Asian people, including Indonesia, consume rice as the main food, therefore maintaining rice productivity is very important. One of the constrain in rice production is the presence of diseases, such as blast disease caused by Pyricularia oryzae or Magnaporthe oryzae, sheath blight disease caused by Rhizoctonia solani, brown leaf spot disease caused by Helminthosporium oryzae or Chochliobolus miyabeanus, bacterial blight caused by Xanthomonas oryzae and Rice Tungro Disease caused by a virus. The severity of the disease depends on the interaction among host plant, pathogen and environment both abiotic and biotic including endophyte, phyllosphere and rhizosphere microbes.

Endophytic microbes are microbes that live in plant tissue without causing symptoms of disease. These microbes play significant role on the health of the host plant and increase the ability of the host plant to suppress directly or indirectly the growth of pathogens in the tissue. They can act as antagonists against pathogens and/or plant growth promoter. As an antagonist, endophytes can produce antimicrobial substances as well as hydrolytic enzymes that directly inhibit the growth and development of pathogen in tissues. In addition, endophytes can also induced resistance of the host plant against pathogens. Trichoderma virens and Bacillus subtillis were found to induce resistance of rice against R. solani.

As plant growth promoting microbes, endophyte can facilitate the acquisitions of resources such as nitrogen fixation, phosphate solubilitation, and iron sesquestering. Endophyte also modulate phytohormones level such as cytokinins and gibberallins, IAA and ethylene.

Considering, the significant roles of endophytes on the plant health and protection, endophytic conservation must be a priority. Rationalisation of the use of pesticides is very important to better preserve microbes. Increasing knowledge and awareness of farmers on the importance of microbial conservation must be done immediately.