Abstract: The medicinal components of Isodon serra were complex and diverse, the effective components were not clear, and the related research at molecular level was very weak. Therefore, constructing the transcriptome database and analyzing it by bioinformatics means could lay a foundation for the research, development and utilization of traditional Chinese medicine. In this study, transcriptome databases of two commonly used Isodon serra source plants and Isodon lophanthoides was conducted, using high-throughput sequencing platform Ilumina, and comparative analysis were conducted. A total of 144 650 Contigs and 103 221 Contigs were obtained from the two species, with N50 values of 1 400 bp and 1 516 bp, respectively. These Contigs were aggregated into 107 777 and 68 220 Unigenes, whose functional annotation analysis focused on the identification of genes and active drug ingredients. There were 14 138 and 11 756 EST-SSR gene sequences in the transcriptome data, respectively. This study not only quickly interpretted the whole genomic information of Isodon serra, but also provided important scientific basis for mining related functional genes, elucidating biosynthesis of active components and their regulatory mechanisms, evaluating germplasm resources and discovering hidden medicinal sites.