Commercial banana cultivars developed from wild species of M. acuminate Colla (A genome) and M. balbisiana Colla (B genome). Whilst wild species are generally seminiferous and fertile, many commercial cultivars are sterile with fruit development resulting from parthenocarpy. As cultivated banana is propagated asexually, its genetic base is narrow with diversity dependent on somatic mutation. Limited genetic variation has resulted in a crop lacking resistance to fungal, bacterial and viral pathogens and numerous pests. Commercial production is often heavily reliant upon agrochemical input. Increased understanding of responses in Musa to biotic stresses will provide new opportunities for genetic improvement. Research is ongoing in characterisation of candidate genes involved in responses to biotic stresses, with groups characterising diverse resistance gene analogs (RGAs) across cultivars and utilising EST approaches for candidate gene discovery. Within our labs, gene discovery is ongoing via analysis of EST data from cDNA libraries produced from Mycosphaerella fijiensis-infected leaf material from M. acuminate ssp. burmannicoides 'Calcutta 4' (resistant) and 'Grande Naine' (AAA genome, susceptible). A large-scale analysis of NBS-LRR RGAs was also conducted in 'Calcutta 4', with polymorphic genetic markers included on a reference map under development at CIRAD. Co-localisation of any RGA markers with QTLs for disease resistance will enable application in marker-assisted selection, facilitating phenotyping for defined traits, such as pest and disease resistance. RGA probes were applied to 'Calcutta 4', 'Grande Naine' and M. balbisiana 'Pisang Klutuk Wulung' BAC libraries revealing numerous putative resistance loci. Shotgun sequencing will provide insight into organisation and evolution of NBS-LRR class R genes in Musa.