Botcinic acid is a phytotoxic polyketide involved in the virulence of the gray mold fungus Botrytis cinerea. Here, we aimed to investigate the specific regulation of the cluster of Bcboa genes that is responsible for its biosynthesis. Our analysis showed that this cluster is located in a subtelomeric genomic region containing alternating G+C/A+T-balanced regions, and A+T-rich regions made from transposable elements that underwent RIP (Repeat-Induced Pointmutation). Genetic analyses demonstrated that BcBoa13, a putative Zn(2)Cys(6) transcription factor, is a nuclear protein with a major positive regulatory role on the expression of other Bcboa1-to-Bcboa12 genes, and botcinic acid production. In conclusion, the structure and the regulation of the botcinic acid gene cluster show similar features with the cluster responsible for the biosynthesis of the other known phytotoxin produced by B. cinerea, i.e., the sesquiterpene botrydial. Both clusters contain a gene encoding a pathway-specific Zn(2)Cys(6) positive regulator, and both are surrounded by relics of transposons which raise some questions about the role of these repeated elements in the evolution and regulation of the secondary metabolism gene clusters in Botrytis.