Blast disease, caused by hemibiotrophic fungus Pyricularia oryzae Sacc. (teleomorph: Magnaporthe oryzae (Hebert) Barr.), previously known as Magnaporthe grisea, is the most serious disease of rice and causes high yield losses in most rice growing regions every year. Almost all commercially grown rice cultivars are susceptible to this disease, and prolonged periods of humid weather will provide favorable conditions for progress of the disease. Blast is an endemic disease in all Iranian and Uruguayan rice fields, with yield losses up to 90 %. Knowledge of different rice blast pathogen populations and factors affecting genetic structure of the isolates in some of main rice growing countries, such as Iran and Uruguay, is still scarce. However, understanding disease epidemiology and plant-pathogen interaction, and finally sustainable disease management is highly dependent on knowledge of the diversity and genetic structure of the pathogen. The genetic variability of 55 P. oryzae isolates from Iran and 32 isolates from Uruguay was analysed using amplified fragment length polymorphism (AFLP). Cluster analysis using different methods based on the AFLP data from 679 monomorphic and polymorphic bands generated with eight primer combinations, was performed. The clustering of the isolates revealed 5 separate AFLP groups among a total of 87 isolates, which typically showed more than 78% fingerprint similarity. Within each AFLP group, three or more haplotypes were detected with a genetic similarity of 100%. Overall genetic similarity was greater than 82% between Iranian and Uruguayan populations. Little evidence for gene flow between the two populations was observed. Analysis of molecular variance (AMOVA) revealed that rice varietal type and geographic region were the dominant factors affecting genetic structure of P. oryzae populations.

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