The postharvest pathogens Colletotrichum coccodes remains quiescent after infection of unripe fruit. However, during fruit ripening, the pathogen assumes a necrotrophic life style, rapidly colonizing the tissue. C. coccodes secretes ammonium during germination and colonization of host tissue that induces host programmed cell death. We further examined the role of ammonia in the infection process by analyzing transcriptome expression from infected and ammonia-treated fruit tissue compared with healthy tissue. The analysis revealed 82 and 237 common upregulated and downregulated genes, respectively. Quantitative reverse-transcriptase polymerase chain reaction analysis of select transcripts in normal and transgenic NADPH oxidase antisense plants revealed that their expression was NADPH oxidase dependent. Common-upregulated genes showed overrepresentation of salicylic acid (SA)-dependent genes as well as genes related to biotic stress. The downregulated genes showed overrepresentation of jasmonic acid (JA)-dependent genes. Indeed, direct application of SA to the fruit enhanced C. coccodes necrotrophic colonization, whereas the application of JA delayed colonization. Importantly, green fruit and red fruit displayed similar gene expression patterns although only red fruit is susceptible to colonization. Thus, it is likely that the resistance of green fruit to C. coccodes colonization is due to additional factors.