Rice blast disease, caused by the fungus Magnoporthe grisea is responsible for considerable damages on rice and leaf spot on some weeds in Iran and in other parts of the world. Infected samples were collected from rice and weeds including Digitaria sanguinalis (crabgrass), Setaria italica (foxtail millet), Echinochloa crus-galli (barnyard millet), and some unknown weeds during 1997-2005 and were preserved in collection of Mycology at the University of Tehran, Iran. In this study, genetic diversity of Magnaporthe grisea species complex isolates was studied based on DNA fingerprinting by rep-PCR, using of two primers including ERIC and BOX. The total DNA of 75 isolates was extracted and DNA fragments were amplified in a thermal cycler program using mentioned primers. Therefore, DNA fragments from 400 bp to 3000 bp were amplified. Based on cluster analysis for two primers (ERIC and BOX), eight fingerprinting groups (ctonal lineages) and sixty haplotypes were identified. "A" clonal lineage was containing the highest number of isolates and became dominant clonal lineages with 35 isolates from rice and 3 isolates from S. italica, whereas the highest number of isolates obtained from D. sanguinalis belonged to "E" clonal lineage and was the second largest clonal lineage. Approximately all of the M. grisea species complex isolates from crabgrass and some of unknown weeds were separated from other isolates in 42% similarity. As a result, asexual fertility causes low diversity in populations of M. grisea species complex and speciation could be one of the reasons of differentiation between isolates from D. sanguinalis with other isolates. Overall, these data indicated a low level of genetic diversity in the Iranian M. grisea species complex population similar to that reported in other countries.