Background: Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropicalAsia as well as northern Australia. It has great economic and ecological importance, with several applications in industryand traditional medicine in many Asian countries. To facilitate further utilization of this plant resource, we present herethe draft genome sequence for B. ceiba. Findings: We assembled a relatively intact genome of B. ceiba by using PacBiosingle-molecule sequencing and BioNano optical mapping technologies. The final draft genome is approximately 895 Mblong, with contig and scaffold N50 sizes of 1.0 Mb and 2.06 Mb, respectively. Conclusions: The high-quality draft genomeassembly of B. ceiba will be a valuable resource enabling further genetic improvement and more effective use of this treespecies.