The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus , which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant. With the purpose of finding novel medicinal compounds and understanding their biosynthetic pathways, we propose to sequence the genome of E. breviscapus . We assembled the highly heterozygous E. breviscapus genome using a combination of PacBio single-molecular real-time sequencing and next-generation sequencing methods on the Illumina HiSeq platform. The final draft genome is approximately 1.2 Gb, with contig and scaffold N50 sizes of 18.8 kb and 31.5 kb, respectively. Further analyses predicted 37 504 protein-coding genes in the E. breviscapus genome and 8172 shared gene families among Compositae species. The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb.