Plantain and banana are important staples for people living in Africa and developed countries, respectively. Both belong to the genus Musa and the cultivated species are all triploids, which spontaneously arose by fusion of the AA and/or BB genomes. This means that nearly all commercial varieties are seedless and propagated exclusively by vegetative means. So far, no detailed information is yet available for the Musa genome that could provide the foundation for understanding the genome structure and extensive characterization of many useful genes. As a first step to gain fundamental insights into the structural and functional organization of the genome, 9216 cDNAs from leaves of plants infected with Mycosphaerella were analyzed from both 5’ and 3’ ends resulting in 8177 (5') and 6132 (3') ESTs. A total of 1264 EST pairs, which showed the same annotation or Genbank ID based on similarity search, correspond to important genes in plants. Among them, 192 ESTs were mapped on the rice genome. In addition, BAC libraries were also constructed from leaves and screened for biotic and abiotic stress responsible genes. Thirteen BACs were sequenced and annotated to clarify the extent of synteny with the rice genome. This analysis could elucidate the major structural characteristics of the Musa genome based on comparison with other monocot plants