Forty monoconidial isolates of Magnaporthe grisea were examined, for an identification of vegetative compatibility group and a characterization of genetic diversity, using rep-PCR genomic fingerprinting. The isolates were collected from weeds Digitaria sanguinalis (crabgrass), Setaria italica (foxtail millet), Echinochloa crus-galli (barnyard millet), and some other unknown ones during 2003 - 2005 and preserved in the Mycology collection of the College of Agriculture and Natural Resources, University of Tehran, Karaj. Nit mutants were obtained from fast growing sectors on Minimal Medium (MM) containing 5-6% potassium chlorate. Complementation between nit mutants of isolates was tested on MM. Three vegetative compatibility groups were determined including VCG1, VCG2 and VCG3, the VCG1 with 29 isolates forming the dominant VC group among others. Genetic diversity of
M.grisea isolates was studied based on DNA fingerprinting through rep-PCR, using two primers previously designed based on ERIC and BOX regions. They generated variable length fragments ranging from 420 to 3000 bp. Phenetic analysis differentiated six distinct clonal lineages designated as A to F. Clonal lineage A with a 62.5% frequency, was the largest fingerprinting group. This study revealed that isolates obtained from foxtail millet and crabgrass were designated in the same VC groups, forming heterokaryons with each other, however these isolates separated from each other the by 42% of similarity using rep-PCR marker. The correlation between VCGs and clonal lineages demonstrated low genetic diversity in M. grisea population within weeds.