Genetic diversity among 63 mango genotypes (Mangifera indica L.) was investigated using Inter-Simple Sequence Repeat (ISSR) markers. A total of 334 scorable amplification products were detected with 28 ISSR primers of which 331 (99.10%) were polymorphic. Most of the primers (89.29%) exhibited 100% polymorphism. Primers UBC-812 and UBC-891 identified with the highest number of genotypes with unique fingerprints (53). The highest number of different fingerprints (58) was obtained with primer UBC-812, while the lowest number of different fingerprints (17) was obtained with primer ISSR-5. Primers UBC-812, UBC-891, UBC-808 and UBC-836 were found to be of high value for fingerprinting in mango as they were able to resolve 58, 57, 55 and 55 of 63 mango genotypes selected for the study, respectively. The Jaccard's similarity values ranged from 0.25 (between 'Cambodiana' and 'Mombasa') to 0.79 (between 'K-1' and 'K-3') with a mean of 0.53. UPGMA tree constructed on ISSR data on the basis of Jaccard's similarity coefficient clustered 55 of 63 mango genotypes into six major groups, however eight mango genotypes remained unclustered. The Cluster 1 comprised of mainly south Indian genotypes, while Cluster 2 comprised of mainly man-made hybrids and genotypes from the Northern and Eastern regions of India. Genotypes indigenous to Western parts of India grouped in Cluster 3. Cluster 4 had the exotic genotypes introduced from Brazil, while Clusters 5 and 6 comprised of Floridan mango genotypes. UPGMA clustering of ISSR data showed good correspondence with pedigree, geographical separation and embryo types, i.e. mono-orpoly-embryonic.