Banana cultivars are derived from hybridizations between species and subspecies of the Musa genus that have diverged in various tropical Southeast Asian regions and archipelagos. Among the diploid and triploid hybrids generated, those with seedless parthenocarpic fruits were selected by humans and thereafter dispersed through vegetative propagation. Musa acuminata subspecies contribute to most of these cultivars. We analyzed sequence data from 24 M. acuminata wild accessions and M. acuminata based cultivars, including diploids and one triploid, to characterize the ancestral origins along their chromosomes. We identified five ancestral groups as contributors to the selected set of cultivars. Four of the ancestral groups corresponded to known M. acuminata subspecies. A fifth group present only in cultivars was defined based on one of them and likely represented more than one uncharacterized genetic pool. Diverse ancestral contributions along cultivar chromosomes were found, resulting in mosaics with at least three and up to five ancestries. This showed that cultivated banana origins involved multiple hybridization steps and were more complex than expected, with yet unidentified ancestors.