Edible bananas are diploid or triploid Musa acuminata, or hybrids of M. acuminata x M. balbisi-ana, producing nutritious seedless fruit of different taste and structure. Breeding for high yield and host plant resistance to pathogens and pests as well as adaptation to abiotic stress of im-portant cultivars is challenging because of seedless and parthenocarpic fruit. In addition, cross-ings and selections of diploid cultivars and wild relatives are severely hampered by transloca-tions and inversions that are widespread in the M. acuminata populations. In this study we pre-sent an overview of cytogenetics, genetics and genomics research carried out to elucidate the meiotic chromosome behaviour in the hybrids and the mapping of genes, and to analyse the dif-ferent classes of DNA sequences in the banana genomes. Finally, we illustrate cytogenetic and linkage mapping of a diploid M. acuminata ssp. malaccensis using the diploid M. acuminata ‘Pa-hang’ as a genome reference and focus on the occurrence of structural rearrangements.