Different Musa species, subspecies, and cultivars are currently investigated to reveal their genomic diversity. Here, we compare the Musa acuminata cultivar Dwarf Cavendish against the previously released Pahang assembly. Numerous small sequence variants were detected and the ploidy of the cultivar presented here was determined as triploid based on sequence variant frequencies. Illumina sequencing also revealed a duplication of a large segment of chromosome 2 in the genome of the cultivar studied. Comparison against previously sequenced cultivars provided evidence that this duplication is unique to Dwarf Cavendish. Although no functional relevance of this duplication was identified, this example shows the potential of plants to tolerate such aneuploidies.