Like many vegetatively propagated crops, most cultivated bananas are highlyheterozygous polyploids of mono or interspecific constitution. During humanselection for edibility over thousands of years, Musa cultivars developed a particularlyhigh level of male and female gamete sterility associated with a low fertilizingpotential making genetic recombination through meiosis and hybridization rareevents during domestication. Recent evolutionary studies in Musa suggest that only afew hybridization events occurred from the wild seedy primitive ancestors to the mostevolved present day cultivars. Unlike other crops, in such a context where the speciescomplex is nearly fixed, banana breeding relies on strategies where an extremelylimited number of crosses are possible. Several genomic tools are now being used todecipher the complexity of the Musa genepool. Molecular markers can distinguishbetween genotypes and have provided a dear understanding of banana domesticationsuggesting only a few hybridization events from the wild seedy primitive to thepresent day cultivars. This allows us to build breeding schemes mimicking thesequence of crossings and selections that occurred over several millennia. The Musagenome can now be explored for desirable genes and subsequent marker-assistedselection. For banana improvement, this approach is particularly important in abiological context of gamete sterility (and difficulties to get large quantities of seeds) for which recombination and implementation of introgression strategies remain thegreatest challenge.