Macrophomina phaseoiina is one of the most prevalent sunflower (Heiianthus annuus L.) pathogens in Egypt. Very little is known about the genetic diversity of this pathogen. Mycelial compatibility test among 18 pathogenic isolates obtained from sunflower plants, showing charcoal rot from different government, showed that isolates of Beni-Sweif could be 2000 considered one mycelial compatibility group. but the remaining isolates gave incompatible reaction. Electrophoresis analysis of 808 protein content of mycelium of all isolates showed the presence of common bands with molecular weights of 16-11 25-26. 28-29. 35- 36. 38-39, 4849. 52-53. 80-81, 74-?5, “(9-80 and 84-85 K.dal among them. These common bands could be used in quantitative determination of such pathogen in soil. RAPD—DNA analysis using two randomized primers. A (Si-CCCGTCAGCA-S“ ) and e (5‘ -CCCGTCAGCA-3‘ ). showed very interesting figure. Four common bands were obtained by primer A, and other three common bands were found with primer 8.