Mendelian genetics has been useful for elucidating qualitative trait variation in Musa. Recent advances in high throughput “omics” technology will provide a means for mapping and gaining insights into complex traits, enabling the translation of genetic information into biological function. Host plant resistance to pests and pathogens, and fruit parthenocarpy are among the most important target traits among the mapping populations available from the Musa Genomics Consortium. In spite of the advances on developing molecular markers and their further use in Musa genetic maps, genetics and breeding research, reports on quantitative trait loci (QTL) mapping are scanty in banana and plantain. Advances made in mapping quantitative traits in Musa are discussed.