The data presented in this article are associated to the research articles, "DOI: 10.1007/s11295-019-1348-3", [1]; and "DOI: 10.1007/s13205-018-1162-x" [2]. Burm. f. and Cav. are medicinal tree plants [3,4] native to Southeast Asia and China, and most members of both the genus and the genus contain various valuable secondary metabolites with a great potential for drug development. Though many phytochemical studies have been conducted using plant extracts from various parts of these plants [4,5], there are very limited genetic resources available. RNA sequencing of and was conducted using pair-end Illumina HiSeq2500 sequencing system, from which the first transcriptome data were produced for both genus and . Transcriptome shotgun assembly using three different assembly tools [2] generated a total of 16,638 non-redundant contigs (N50, 900 bp) from and 7,857 (N50, 423 bp) from . The data are accessible at NCBI BioProject: PRJNA428402 for [2] or PRJNA435648 for [1].