RAPD and AFLP markers are used to characterize germplasm in several important crop species. Both RAPD and AFLP analyses confirm that variation observed at the morphological level in various ‘Carabao’ mango strains also exists at the molecular level. RAPD and AFLP DNA markers improve the effectiveness of testing for genotype differences. They can serve as genetic fingerprints of individual varieties and genotype and can be very important in establishing the unique identities of genetic strains. This developed technology may be useful to researchers and mango orchard growers.