Participatory Rural Appraisal (PRA) method was used to identify seventeen Musa cultivars that were rated highly by the small-scale farmers in Kenya. The cultivars were studied alongside five reference cultivars of genomic groups AA, AB, AAA, AAB, and ABB. This investigation was done to uncover the genomic groups prevalent among the Kenyan cultivars, as well as sort out synonyms to enable in vitro production of true-to-type plants. Random Amplified Polymorphic DNA (RAPD) markers with ten 10-mer primers was used for molecular characterization. The primers generated sixty-nine genetic markers that were used in estimation of genomic groups and cultivar identification. Pairwise RAP Distance analysis of the data and subsequent generation of a genogram using the ‘Neighbor Joining Tree’ programme grouped the cultivars into two major clusters depending on their genomic similarities. One cluster comprised of the Kenya-highland bananas, which grouped with the AAA reference cultivar ‘Poyo’. The other cluster contained the coastal lowland cultivars, which grouped with the ABB, AAB, and AB reference cultivars ‘Saba’, `Kelong Mekindu`, and `Safet Velchi’ respectively. The dissimilarity analysis between the samples did not indicate duplication among the banana accessions. Each cultivar was genotypically different although some were closely related.