Herein we report a study examining the effects of colletotrichumine A, an indole-pyrazine alkaloid isolated from the anthracnose pathogen Colletotrichum capsici, on chilli plants. A colletotrichumine A-pathogen combination was more toxic to the host than individual inoculations of colletotrichumine A or the pathogen. The colletotrichumine A-pathogen combination led to an increased activity of defense related enzymes viz. PPO and SOD, while levels of the lignification enzymes PAL and PO decreased. Higher levels of phenols including catechin and ferulic acid were also observed with the colletotrichumine A-pathogen combination compared to individual treatment. The likely role of colletotrichumine A during chilli anthracnose infection is supported by histochemical analysis of infected plants that showed increased cell death after infection.