Black Sigatoka is a major disease of East African highland cooking bananas in Uganda. Aqueous extracts of Azadirachta indica, Cinnamomum zeylanicum and Capsicum annuum have shown the potential to reduce Black Sigatoka in banana plantlets. The mechanisms by which plant extracts confer protection against plant pathogens has previously been reported to involve activation of defence and direct antimicrobial activity. In the current study, both antimicrobial activities of selected extracts were studied as well as expression of three defence-related genes using quantitative real-time PCR. Gene expression was compared in susceptible (cv. Musakala, genomic group AAA-EA) and resistant (cv. Kayinja, genomic group ABB) banana cultivars. Additionally, Musakala treated with A indica extract at 1 day before inoculation (DBI) was tested for induction of defence-related genes at 0, 10 and 20 days after inoculation (DAI). Pathogenesis-related genes (PR-1 and PR-3) and non-expressor of PR-genes (NPR1B) were up-regulated in the resistant cultivar. The genes analysed responded at late time points to M. fijiensis inoculation in both extract-treated and control plants in the susceptible cv. Musakala. On the other hand, A. indica and C. annuum completely inhibited mycelial growth of M. fijiensis at 30% (w/v). These findings suggest that the effect of plant extracts on Black Sigatoka is strongly associated with the direct antimicrobial effects.