Edible bananas originated mainly from two wild species, Musa acuminata and M. balbisiana, and recombinations between chromosomes occur in polyploid varieties. Jeridi et al. compare homoeologous pairing in a diploid interspecific variety and in its allotetraploid derivative obtained from induced chromosome-doubling. Analysis of chromosome associations at both ploidy levels suggests that the newly formed allotetraploid behaves as a ‘segmental allotetraploid’ with three chromosome sets in a tetrasomic pattern, three sets in a likely disomic pattern and the five remaining sets in an intermediate pattern. The segmental inheritance pattern exhibited by the allotetraploid genotype implies chromosome exchanges between M. acuminata and M. balbisiana species and opens new horizons for reciprocal transfer of valuable alleles.