Five isolates of the Aspergillus flavus, were isolated from Mangrove soil of Ras Mohammed protected area at Sharm El-Sheikh, Egypt. Assiut University Mycological Centre (AUMC), Egypt, identified the fungal strains and deposited in AUMC with their accession numbers. Two molecular marker systems, four SCoT primers (Start codon targeted polymorphism) and six ISSR primers (inter-simple sequence repeat) were employed for identification and genetic relationship between five indigenous Aspergillus isolates. A total of 62 and 48 amplicons were detected by four SCoT and six ISSR primers, among which 57% and 52.35% bands were polymorphic respectively. The genetic similarity among the species ranged from 0.60 to 0.86 using SCoT and 0.74 to 0.94 using ISSR marker systems. Based on the marker analysis all the five isolates were clustered into three major groups for ISSR primer and SCoT primers. Cluster analysis also reveals high genetic variation among the genotypes

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