Forty eight mango hybrids were analyzed using 17 simple sequence repeat (SSR) markers. Which detected 59 scorable loci, of which 45 were polymorphic. The size of the alleles detected ranged from 100 to 480 bp. SSR markers was highly polymorphic with an average of 3.47 alleles per primer. SSRs gave moderate values of Polymorphis Information Content (PIC) and heterozygosity. The genetic relationship among mango hybrids, based on Jaccard's Similarity Coefficient values ranged from 0.38 (between H-1-13 and H-6-8) to 0.97 (between H-13-4 and H-13-7). The dendrogram, based on UPGMA cluster analysis, grouped the mango hybrids into three major groups. Cluster 'A' comprised of the five most diverse hybrids, namely, H-12-2, H-9-6, Pusa Arunima, H-9-5 and H-1-13. Two unique fingerprints were identified in hybrid H-9-6. The size of unique fingerprints ranged from 90 (MiSHRS-18) to 350 bp (MiSHRS-39). The Principal Coordinate Analysis also exhibited more or less similar distribution of mango hybrids. The tendency of clustering among mango hybrids revealed that they had stronger affinity towards female parent Amrapali.