Rare and endangered plants are important plant resources in nature， and play a key role in the study of plant phylogeny， ecosystem restoration， plant stress resistance physiology， and the excavation of stress-resistance genes. However， the lack of genetic information has severely restricted the conservation and utilization in most endangered plant. Due to the large genomes， complex genetic information， and unclear genetic backgrounds of endangered plants， it is relatively difficult to sequence the genomes of endangered plants. In recent years， RNA-Sequencing could directly sequence non-reference genomic species， what makes it to be widely used in the study of endangeredplants. In addition， this paper presented the prospect of the application of RNA-Sequencing technology in the study of endangered plants and suggested the new ideas of transcriptome using in the endangered plants in future.