In this study twenty six RAPD primers and six ISSR primers were used to assess the genetic diversity among seven pecan genotypes cultivated in Egypt. Using the RAPD and ISSR analyses, 156 out of 276 and 30 out of 59 alleles, respectively, were detected as polymorphic markers among the seven pecan genotypes. The pecan genotypes were characterized by 59 genotype-specific markers i.e 45 for RAPD and 14 for ISSR that would be considered as useful markers for pecan genotypes. Eleven markers distinguished the Grazona genotype, five markers for the Cheyenne genotype and one marker for each of Desirable genotype, Mahan and Moneymaker.