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Bananas and plantains are edible and vegetatively propagated parthenocarpic species of the genus Musa. They are used as staple food, dessert and cash crop by more than hundred millions of people throughout the world. However, the crop is threatened by several pests and diseases in central and eastern Africa. One way of partly solving this problem is to have diploids which have desirable traits currently lacking in the AAA-Lujugira-Mutika subgroup. The study assessed through 21 microsatellite markers pairs the cladistic closeness of the diploid AA-Mshale accessions with AAA-Lujugira-Mutika with the purpose of inclusion in breeding programmes. Results showed that the eight studied accessions of AA-Mshale were different from each other. AA-Mshale malembo was fairly well established to be among the ancestor of Lujugira-Mutika, suggesting the determinism of its pollen viability and the level of resistance to pests for including in breeding programmes. The use of two pairs of microsatellites per chromosomes linkage group established the existence of alleles’ deletion, recombination or non-annealing. The closeness among AA-Mshale and AAA-subgroups (Ibota, Gros Michel and Green Red) so far established through other techniques was confirmed. The results recommend the use of microsatellite markers, covering 11 linkage groups for cultivar identification and diversity study.