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Verticillium dahliae Kleb. is a necrotrophic plant pathogen that causes serious soil‐borne vascular disease in cotton. The molecular basis of cotton response to this pathogen is poorly understood. To capture a wide spectrum of differentially expressed genes in the cotton defence response, RNA isolated from Gossypium barbadense was employed to generate highly enriched transcripts by polymerase chain reaction (PCR)‐select suppression subtractive hybridization (SSH). A total of 211 unique genes were differentially identified and classified into 11 functional categories. The largest groups contain genes involved in metabolism, stress/defence response, cell structure and signal transduction. More than one‐third of the genes (38%) were identified as unknown classification or function. Northern blot analysis and quantitative real‐time PCR (qPCR) were performed to investigate the expression patterns of some …