Despite the economic importance of Eucommia ulmoides for rubber production and for traditional Chinese medicine，our knowledge of its genome remains limited. Here we present a high-quality genome assembly（1.18Gb，scaffold N50=1.88Mb） for E. ulmoides by integrated sequencing and assemble strategies，the first sequenced genome from the order Garryales. The sequencing sample were collected from an wild individual in Shennongjia. By integrating the results from de novo，homologous，and transcriptional predictions，we annotated 26，723 protein-coding genes. In E. ulmoides，the farnesyl diphosphate synthases 1，3，and 5 synthesize long-chain trans -polyisoprene（TPI） in contrast to cis -polyisoprene in Hevea brasiliensis. Despite the expansion of the REF/SRPP （rubber elongation factor/small rubber particle protein） gene family，only SRPP1 was associated with TPI biosynthesis in E. ulmoides . Phylogenetic ananlyses indicated the rubber biosynthesis was independently originated in E. ulmoidesand H. brasiliensis，further suggesting that the polyisoprene biosynthesis in eudicots was polyphyletic in origin. The outstanding resistance/tolerance and high content of bioactive compounds of E. ulmoides might be attributable to expanded gene families and highly expressed genes involved in stress and secondary metabolites biosynthesis. Our results provide valuable resources for understanding TPI biosynthesis as well as stress response mechanisms，and will facilitate the genetic improvement and biological study of E. ulmoides .