Pistacia chinensis subsp. integerrima is one of the medicinal plants, well known for gall formation and popularly used in Ayurveda to treat various systemic diseases such as chronic disorders, respiratory problems, etc. P. integerrima genome characterization will aid in the study of Pistacia genes and pathways involved in therapeutic application. To understand the biological characteristics of this plant and to gain the genetic insight into the biosynthesis of its natural compounds, the whole genome of P. integerrima and its leaf transcriptome was sequenced using Illumina sequencing technology. The sequenced genome was functionally annotated, and gene prediction was performed with integrated genome annotation workflow. The pathway analysis was carried out using KEGG database. We obtained a draft genome assembly of 462 Mb with N50 16,145 bp. A total of 39,452 genes were found, and 18,492 of these contained RNA or protein evidence. We characterized the genes involved in biosynthetic pathways of different plant secondary metabolites such as flavonoids and terpenoids. Also, we identified miR397 and miR828 family noncoding RNA; which mainly targets the laccase (LCA) and MYB protein functioning respectively. Phylogeneic analysis showed that P. integerrima is genetically more closer to P. vera. In this study, we attempt to explore the whole genome information of P. integerrima which will provide a genomic insight in the future for omics studies as well as serves as valuable resource for the molecular characterization of medicinal compounds.