In the present experiment the universal primer ITS (Internal transcribed spacer) were used to access genetic relationships among three Aspergillus species viz. A. niger, A. flavus, A. candidus. Four ITS primer namely ITS-1, ITS-2, ITS-3 and ITS4 were used to gain rapid and precise information about genetic similarities and dissimilarities of different Aspergillus species. Among all primers used ITS-1 and ITS-4 were more reproducible and show high level of polymorphism.