The fungus Cochliobolus sativus is the causal agent of barley common root rot disease. Twenty-two isolates of diverse geographical origin within Syria were studied in relation to pathogenicity, analysis of genomic DNA through random amplified polymorphic DNA (RAPD) and variation within the nuclear rDNA [internal transcribed spacers (ITS)]. The data demonstrated that variation occurred in the pathogenicity to isolates and in the resistance level among genotypes. The isolates were highly variable and 11 unique haplotypes using RAPD and nine using ITS-RFLP were identified. The molecular parameters used showed that C. sativus isolates reside in three phylogenetic groups. Unweighted pair-group method with arithmetic averages analysis did not result in any clusters or clades specific to origin or pathogenicity. However, most of isolates with different pathogenicity levels shared the same clades. The phylogeographic distribution pattern suggests a regional dispersal of C. sativus.