Abstract Cotton plants accumulate gossypol and related sesquiterpenoids in pigment glands as their defensive machinery against pathogens and herbivores. However, the accumulation of gossypol, which is toxic and antispermatogenic, also makes it hard to use cottonseeds for human and animal consumption. Detailed understanding of gossypol biosynthesis and its regulation should provide better strategies for resolving this problem. Recent progresses have been made to dissect gossypol pathway at molecular level. Genes encoding farnesyl diphosphate synthase (geranyltranstransferase), (+)-δ-cadinene synthase (CDN1 or CAD1), (+)-δ-cadinene-8-hydroxylase (CYP706B1), and S -adenosyl-L-Met: desoxyhemigossypol-6-O-methyltransferase, have been isolated, and their expression patterns analysed. A WRKY transcription factor from Gossypium arboreum , GaWRKY1, was found to activate CDN1-A gene expression through binding to W-box palindrome on the CDN1-A promoter. A laccase, GaLAC1, which might be involved in the later steps of gossypol biosynthesis, was also identified. In addition, a necrosis- and ethylene-inducing protein from Verticillium dahliae , VdNEP, was found to be involved in the interaction between cotton plants and the fungal pathogen. The expression of these genes has been studied under different developmental stages, and under treatment of fungal elicitor preparation. Antisense inhibition of CDN1 gene expression has reported to result in reduced gossypol accumulation in cottonseed to a varied degree. (+)-δ-Cadinene-8-hydroxylase, encoded by a single copy gene in the cotton genome, might be a better alternative for genetic engineering to specifically deplete gossypol biosynthesis/accumulation from cottonseeds.