To detect DNA polymorphism among isolates of the rice blast fungus Magnaporthe grisea, the AFLP (amplified fragment length polymorphism) technique was adopted. When each primer combination of EcoRl-AC/MseI-CA, EcoRI-AA/MseI-CA or EcoRI-AT/MseI-CA was used, every M. grisea isolate produced more than 30 fragments. The number was approximately 10 to 20 times higher than that for the RAPD technique using 10-nucleotide random primers. Moreover, in every primer set, 5 isolates from independent clonal lineages were distinguishable from each other by fragments showing polymorphism. On the other hand, 5 isolates including an original isolate and its pathogenic mutants produced the same number and size of amplified fragments in all 6 primer sets (the above plus EcoRI-AC/MseI-CC, EcoRI-AA/MseI-CC and EcoRI-AT/MseI-CC). These results show the higher utility and reproducibility of the AFLP technique in elucidating the ecology of rice blast fungus.