To date, only natural rubber produced by Hevea brasiliensis Muell. Arg, a member of the family Euphorbiaceae, has been widely used. However, current understanding on the basic biology of H. brasiliensis, including the mechanism of natural rubber biosynthesis, is far from complete. To provide genomic resources for the improvement of the agronomic traits of this rubber tree, whole-genome sequencing and cap analysis gene expression (CAGE) studies were carried out. H. brasiliensis clone RRIM 600, one of the most popular clones that was widely planted in Malaysia from the 1960s to 1970s, was selected for whole-genome sequencing. The genome of H. brasiliensis RRIM 600 was assembled based on ~160-fold combined coverage of Illumina and PacBio reads. To understand the transcriptional control of H. brasiliensis genes, CAGE approach was used to analyze the transcription start sites (TSSs) of genes expressed in different tissues (bark, leaf and latex). In total, 484 million CAGE tags were sequenced which allowed the identification of 2,948,134 potential TSSs.