Objective: The aim of this study was to estimate Genetic variability and phonetic relationships of 50 isolates of P. sojae from Iran.Methods: During 2005–2007, 142 isolates of Phytophthora sojae were collected from soil samples and diseased soybean plants from Lorestan, Mazandaran, Golestan and Ardabil provinces. Races of the isolates were determined. DNA of P. sojae fifty isolates was amplified with 20 RAPD and 5 ISSR primers.Results: Five primers amplified 77 fragments, of which 20 were polymorphic, indicating low variability. RAPD and ISSR primers clustered isolates into three distinct groups at 85% similarity. Genetic Diversity among isolates detected intra specific variability even among isolates of the same geographic origin. There is no correlation between races, geographical distribution, and molecular markers.