Aflatoxin contamination of peanut seeds , results from growth in kernels by toxigenic strains of the fungus Aspergillus flavus Link. This can occur in the field (Pre-harvest) when severe late - season drought stress occur and during storage (post - harvest) when improper conditions of moisture and temperature exists. Current investigations aims the detecting A. flavus in commercial peanuts production area, moreover, some isolated mycoflora were found to be associated with seeds during (2006-2007) growing seasons. Analyses of 198 seed samples recorded (13.1%) aflatoxin contaminated kernels belonging to 26 samples with aflatoxin detectable levels ranked from (1.6 – 40) ppb. A. flavus total DNA from both toxigenic and non-toxgenic isolates obtained from seeds or soil at five geographic locations was subjected to RAPD technique (random amplified polymorphic DNA). Phonetic and caldistic analyses of the data, based on bootstrap analyses, indicated that the RAPD system was unable to distinguish between aflatoxigenic and non aflatoxigenic A.flavus strains. Therefore, the present study supports the application of that technique for strain characterization and  preliminary evolution.