Species of Colletotrichum cause devastating diseases on many crop plants worldwide. These fungal pathogens use a hemibiotrophic infection strategy that involves the formation of specialized cell-types adapted for initial penetration (appressoria), growth inside living plant cells (biotrophic hyphae) and tissue destruction (necrotrophic hyphae). The genomes of 4 species were sequenced to date: C. higginsianum (Ch), C. graminicola (Cg), C. orbiculare (Co) and C. fructicola, which respectively infect Arabidopsis, maize, cucurbits and strawberry. All 4 genomes encode extraordinarily large inventories of plant cell wall-degrading enzymes, with the three dicot pathogens having twice as many pectinases as the monocot pathogen C. graminicola, reflecting adaptation to hostcell wall composition. Genes encoding secondary metabolism (SM) enzymes, especially those involved in synthesis of polyketides, terpenes and alkaloids, are also highly expanded compared to other sequenced fungi, suggesting Colletotrichum species are capable of great chemical diversity. Similar to biotrophic pathogens, all 4 species encode large repertoires of putative secreted effector proteins that likely function for host manipulation. The transcriptional dynamics underlying hemibiotrophy were examined using RNA-Seq (Ch, Cg) and microarrays (Co). Although appressoria formed in vitro resemble those in planta, comparison of their transcriptomes showed >1,500 Ch genes are induced only upon host contact, suggesting that plant signals sensed by appressoria reprogram fungal gene expression in preparation for host invasion. SM enzymes and secreted effectors are among the most highly induced genes in appressoria and biotrophic hyphae, suggesting a role for these infection structures in host manipulation. At the switch to necrotrophy, genes encoding a vast array of wall-degrading enzymes, proteases and membrane transporters are up-regulated, enabling the fungus to mobilize nutrients from dead and dying cells to fuel its rapid growth and sporulation. In Ch, the majority of putative effector genes are plant-induced and expressed in waves, suggesting distinct suits of effectors are deployed at each infection stage. Observation of RFP-tagged effectors by confocal microscopy and TEM-immunogold labelling showed that early-expressed effectors are focally secreted by appressoria, before host invasion, through the basal penetration pore, suggesting appressoria function in effector delivery in addition to penetration. Effectors secreted by biotrophic hyphae accumulate in novel compartments called ‘interfacial bodies’ on the hyphal surface, but were not detectable in the plant cytoplasm. However, transient expression in planta of 60 effectors as N-terminal fusions with GFP revealed 12 are targeted to the plant nucleus or other organelles while 3 decorate plant microtubules, suggesting some effectors are translocated into host cells