Plant endophytes spend at least part of their life cycle in plants without causing diseases in the hosts, being the microbial resources with rich species and diverse functions. With the advancement in sequencing technology, the microbiological study of endophytes has become increasingly intensive. Being praised for the targeted validation and low cost, Sanger sequencing has been preferred by researchers. However, Sanger sequencing is no longer suitable for deeper genomic study of endophytes due to the low throughput. In this paper, we briefly summarize the research history of endophytes, review the applications of next-generation sequencing characterized by high throughput and third-generation sequencing (single-molecule real-time sequencing) in the research on endophytes, and summarize the research results of different sequencing technologies. Furthermore, we summarize the advantages and limitations of different sequencing technologies and discuss how to choose the appropriate sequencing technology according to the research needs. This review provides a reference for researchers to further explore the potential value of plant endophytes.
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