Cultivated bananas are the result of hybridisation between wild species and subspecies of Musa that diverged in the region of Southeast Asia and New Guinea. These hybridisations produced diploid and triploid hybrids, some of which yielded parthenocarpic seedless fruit, which were selected and propagated by humans. As a result, banana genomes are complex mosaics of large blocks of sequences involving nine genetic groups including one unknown contributor. We generated continuous genome assemblies of these contributors including a hybrid that provided access to part of the unknown ancestor's genome. Comparative genomic and phylogenetic analyses between those genomes revealed chromosomal rearrangements and centromere diversification. The centromeric regions have incorporated different types of repeated sequences, notably tandem rDNA repeats that may reduce fertility in hybrids. Chromosome rearrangements are mainly reciprocal translocations, sometimes with complex structures, that reduce recombination in structural hybrids and were generally found preferentially transmitted to progenies. These factors could contribute to an ongoing speciation process within Musa by reinforcing reproductive isolation, which probably originated from past fluctuations in climatic conditions and land connections in the Southeast Asia/New Guinea region.