The Malaysian Pepper Transcriptome Sequencing (MPTS) project is a database containing transcriptome and associated EST for Malaysian pepper varieties. It is a continuously updated catalog of pepper genes and genetic disorders. In the first stage of this project, we provide an exon-level transcriptome data generated using illumina HiSeq 2000 System from 26 tissue samples sampled from both leaves, flower and fruit of pepper plants. Samples range from different developmental stages from flower to fruit as well as pepper challenged with disease. MPTS is authored and edited at the Research and Development Division, Malaysian Pepper Board, Kuching, Sarawak, Malaysia.