Ramularia collo-cygni (Rcc) causes Ramularia leaf spot (RLS) disease of barley. The fungus develops asymptomatically within its host until late in the growing season when necrotic lesions become visible on upper leaves. Fungal secondary metabolites (SMs) have been proposed as important factors in RLS lesion formation, but the biosynthetic pathways involved remain largely unknown. Mining the Rcc genome revealed the presence of ten polyketide synthases (PKSs), ten non-ribosomal peptide synthetases (NRPSs) and three hybrid PKS-NRPS (HPSs) identified within clusters of genes with predicted functions associated with secondary metabolism. SM core genes along with their predicted transcriptional regulators exhibited transcriptional co-expression during infection of barley plants. Moreover, their expression peaked during early stages of host colonisation and preceded or overlapped with the appearance of disease symptoms, suggesting that SMs may manipulate the host to promote colonisation or protect Rcc from competing organisms. Accordingly, Rcc inhibited the growth of several fungi in vitro, indicating it synthesised and excreted anti-fungal agents. Taken together, these findings demonstrate that the Rcc genome contains the genetic architecture to synthesize a wide range of SMs and suggests that co-expression of PKSs and HPSs is associated with competitive colonisation of the host and early symptom development.