Species of the fungal genus Colletotrichum cause devastating diseases on numerous major crop plants worldwide. C. higginsianum attacks cultivated members of the Brassicaceae but also the model plant Arabidopsis. Initial host cell invasion requires the differentiation of a specialized cell-type called an appressorium that mediates penetration of the plant cuticle and cell wall. Compared to other sequenced ascomycetes, the genome of C. higginsianum contains an exceptionally large number of genes (89) encoding secondary metabolism (SM) key enzymes. These are organized into 68 gene clusters which, as in other fungi, also contain genes encoding accessory enzymes of the same biosynthetic pathway, together with efflux transporters and pathway-specific transcription factors. A remarkable finding from transcriptome profiling was that 19 SM clusters are specifically expressed only at early stages of plant infection inside appressoria. Since each cluster potentially synthesizes one metabolite, this suggests fungal appressoria deliver a cocktail of different chemicals to the first infected host cell. At this early stage host cells remain alive, raising the possibility that these molecules function similar to protein effectors for host manipulation, rather than as simple phytotoxins. We present evidence that the coordinated and stage-specific expression of SM genes is orchestrated at two levels, namely remodelling of chromatin structure and regulation by global transcriptional activators. Progress towards the functional characterization of these metabolites will also be presented, including evidence that some metabolites can subvert plant immune responses.