Lisianthus (Eustoma grandiflorum) is an important ornamental plant native to North America. So far, the number of basic molecular research reports on Lisianthus is relatively small, especially the research related to the molecular mechanism of response to drought stress. In this experiment, transcriptome second-generation sequencing technology was used to study Lisianthus seedlings under drought stress. The results showed that the transcriptome sequencing data had good quality control results. In order to obtain genetic information on this basis, the sequences were spliced using software such as Trinity and Corset, a total of 102,014 non-redundant genes were obtained, including 2,929 coding genes which were found to belong to 79 transcription factor families after analyzing. Annotating all genes, Zhongguo coffee was found to be the species with the highest comparison similarity. Finally, simple sequence repeat (SSR) analysis was performed on the gene sequences, and all SSR information contained in non-redundant genes and transcription factor coding genes had been obtained. The results of this study can provide candidate molecular resources for subsequent studies on Lisianthus 's response to drought stress in the future.