The first step towards improving mango production was started by the selection of eleven genotypes because of their superior horticultural characteristics and fruit quality parameters, from Suez Canal University orchard through 2016 to 2018 seasons. All studied mango genotypes (G) differed in dates of full bloom, maturity stage, bearing habit, floral malformation and fruit characteristics. All genotypes had commercially acceptable qualities and produced relatively high yield ranged from 298.7 - 394 Kg/tree. Generally, genotype No. 9 recorded the highest value (96.6%) in the general evaluation according to yield, Biennial bearing and fruit quality, followed by genotypes No. 7 and No. 5 which scored 94.0 and 91.8%, respectively. In general, these three genotypes possessed most of the desired commercial attributes of international standard. In addition, further understanding of the structure of genetic diversity was done using nine SSR markers based on their scorability, repeatability and capability to differentiate among studied genotypes. Also, analyze of DNA fingerprinting data to create molecular IDs was done to get an idea for the conservation and protection of studied genotypes. The nine SSR loci produced a total of 32 alleles with 97% polymorphism and observed alleles per locus diversified from 1 to 8 alleles with an average of 3.6 without zero alleles. The observed heterozygosity (Ho) within the loci ranged from 0.0 to 0.55 with an average value of 0.23, heterozygosity level within the genotypes varied from 0.11 to 0.44. The polymorphic information content (PIC) values ranged from 0.0 to 0.86 with an average value of 0.49, whereas the mean of discriminating power (DP) for all loci was 0.51. Regarding the probability of matching fingerprints, none of the genotypes were different or similar at all loci with any of the rest genotypes and this value ranged from low to medium with an average of 0.48. The similarity degree ranged from 0.18 to 0.90 with an average of 0.53, indicating that the genetic differences were moderate among mango genotypes under study. Whereas, seven of these genotypes produced 11 unique bands maybe accompanying to  number of novel functional alleles, which can be used in mango improvement.