Aspergillus niger is one of the most common species of the genus Aspergillus with a wide distribution and multiple hosts. Given the importance of this species in the economy, health and hygiene, the identification of this species is important, although morphological identification methods are suitable for detecting Aspergillus species, they are generally ineffective in identifying the races and populations of species of this genus. therefore some molecular techniques are using to dissolve this problem, In this study, isolated population of Aspergillus niger form five crops including: Wheat, Barley, Corn, Soybean and Rapeseed, identified by morphological methods. To determine of genetic diversity of that population, twenty standardized primers based on ISSR method used. SPSS, GeneAlex and PAST software use to statistical analysis, The results of statistical analysis based on ISSR findings showed, using this method, Aspergillus niger varieties isolated from different hosts and different regions can be distinguished from each other.