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Northeast India is known for its diverse nature of soil, climate, and topography that supports rich banana diversity. Banana (Musa sp.) is the second most important fruit crop in India due to its availability throughout the year, taste along with the nutritive and medicinal value. Thus, the genetic diversity of banana resources is essential for present and future food. This study aimed to determine the comparative genetic variation among 14 non-commercial edible banana cultivars of Assam, India, by using 50 different morphological characters with ISSR markers. Morphological data were analyzed hierarchical clusters and principal coordinates which showed to cluster all the accessions into two distinct groups and subsequently into four subgroups. Furthermore, ISSR markers revealed the average percentage of polymorphism. A total of 62 bands were detected of which 56 bands showed polymorphism using seven primers. The highest number of the band was detected with the primer UBC-843 and the lowest number of the band was observed with UBC-848. The genetic similarity index was prepared using Jaccard's similarity coefficient and the range of genetic similarity was from 0.28 to 0.77 with 0.51 of average. Dendrogram produced from the cluster analysis showed the clear division of the genotypes into two distinct clusters. Seven accessions of viz. Bharatmoni, Assamiya-malbhog, Gobin tulashi, Bokmoni, Bangali-malbhog, Katiya-jahaji, and Abor-malbhog were clustered in the first group. The second group included the accessions viz. Jatikol, Adeel, Guwahatia-kol, Fessa-monohar, Athiya kol, Ximalu-monohar, and Bogi-monohar. The Mantel test analysis also showed positive relationships between morphological traits and ISSR markers. [ABSTRACT FROM AUTHOR]