The Fusarium species that is the cause of the disease that we used in our study takes an important place among microfungi that cause disease in agricultural plant species and economic loss. The subgroups and races of this species especially cause diseases with various symptoms on cereals such as wheat, barley, corn and clover, on fruit trees, and garden and ornamental plants. The definition of these microfungi that are pathogens at the genetic material level is important in terms of determining the disease they cause. The aim of the present study was to determine the genetic relationship among twenty isolates of Fusarium spp. (18 Fusarium species) isolated from wheat, maize and clover in Turkey using RAPD technique. In the present study, Random Amplified Polymorphic DNA (RAPD) markers were used to assess the genetic diversity within 20 isolates of Fusarium. RAPD analysis was performed with 16 decamer primers selected from a total of 30 primers. A total of 408 reproducible fragments were amplified by 16 RAPD primers. All the fragments were polymorphic (100%). The size of these fragments ranged from 100 to 3000 bp. The number of bands per primer varied between 14 and 39. Similaritiy indexes were calculated to determine the genetic relationships among these populations and subsequently dendograms based on Unweighted Pair-Group Method using Arithmetic Averages (UPGMA) was derived. Based on DNA finger prints, all isolates of Fusarium were categorized into three major clusters. The results demonstrated that RAPD analysis can be used for assessing the genetic diversity and the relationships among the Fusarium species.