Despite the advances made for genetically improving this vegetatively propagated crop, many challenges remain. Banana production faces major challenges from biotic and abiotic stresses. This is aptly summarized by Heslop-Harrison and Schwarzacher (2007) that in addition to the critical need for better genetic resistance to pathogens and pests, there is the need for banana to contribute to better food security through greater yields and more effi cient production, greater yield stability, better use of water, less toxic chemical input, and higher quality. In this chapter we examine some of the issues facing the genetic improvement of Musa and suggest proposals for future research areas in the crop.