Alternaria brassicicola is the causative agent of black spot disease of Brassicaceae belonging to the genera Brassica and Raphanus. During host infection, A. brassicicola is exposed to high levels of antimicrobial defence compounds such as indolic phytoalexins and glucosinolate breakdown products. To investigate the transcriptomic response of A. brassicicola when challenged with brassicaceous defence metabolites, suppression subtractive hybridization (SSH) was performed to generate two cDNA libraries from germinated conidia treated either with allyl isothiocyanate (Al-ITC) or with camalexin. Following exposure to Al-ITC, A. brassicicola displayed a response similar to that experienced during oxidative stress. Indeed, a substantial subset of differentially expressed genes was related to cell protection against oxidative damage. Treatment of A. brassicicola conidia with the phytoalexin camalexin appeared to activate a compensatory mechanism to preserve cell membrane integrity and, among the camalexin-elicited genes, several were involved in sterol and sphingolipid biosynthesis. The transcriptomic analysis suggested that protection against the two tested compounds also involved mechanisms aimed at limiting their intracellular accumulation, such as melanin biosynthesis (in the case of camalexin exposure only) and drug efflux. From the Al-ITC and the camalexin differentially expressed genes identified here, 25 were selected to perform time-course studies during interactions with brassicaceous hosts. In planta, up-regulation of all the selected genes was observed during infection of Raphanus sativus whereas only a subset were over-expressed during the incompatible interaction with Arabidopsis thaliana ecotype Columbia