During the last 30 years, plant endophytes deserve more attention around the world although its definition still remains confused and controversy. In this review, major historic events in endophyte researches and their scientific significances were discussed. Scientists firstly focused on special roles of endophytic fungi within woody plants and Gramineae plants. After anticancer natural product taxol was found to be produced by a plant endophytic fungus in 1993, biologically active metabolites were widely screened from plant endophytic microbes in many countries. Though comparing and contrasting the endophytes from different tissues of annual grasses, perennial grasses, woody plants and vine plants, common and specific properties of these endophytes were reviewed. The tendency of researches on endophytes were revealed. Plant endophytes contributed a lot to the total amount of microbe species on the earth. This review pointed that “the real situation of plants in the nature were microbes-plants symbiota”. Therefore, plant breeding were actually improvement of microbes-plants symbiota. Finally, the influences of endophytes on the ecology, biology, microbial evolution, species formation, plant-endophyte co-metabolism, plant protection, animal husbandry, veterinary science, forestry and some other fields were also discussed. Endophyte researches exhibit another view of microbial resources, significant impacts should be observed in many areas. The significance of endophytes not only rely on their niche, the ecological characterics, but also the synergism between endophytes and their hosts, resulting some new functions and new metabolites due to the co-metabolism and interactions.