Value of the Data •Capsule rot disease, commonly known as Azhukal disease is reported to be one of the most serious fungal diseases in small cardamom caused by Phytophthora meadii [1] often leading to annual loss of 30–40% [2]. •Under fungal infections R genes and many other defense related genes triggering disease tolerance to plants may get over expressed. •Transcriptome data generated from leaves of plants grown under specific conditions could provide information on molecular mechanism underlying disease tolerance. •Differential expression analysis of control and treated cardamom could compare the expression variation of particular genes in normal and diseased plant grown under similar conditions.