Eighty-nine isolates of Magnaporthe grisea collected from rice plants in 9 provinces/cities of China and 7 isolates collected from 6 countries of Brazil (BR), Cameroon (CM), Madagascar (MD), Mali (ML), Philippines (PH), Thailand (TH) provided by The International Center for Collaboration in Agronomic and Development (CIRAD) as a control were tested for mating type with 4 hermaphroditic fertile isolates MAT 1.1 (KA3 and TH12) and MAT 1.2 (Guy11 and TH16). Using microsatellite markers to analyze the relationships between fertile isolates and their genetic diversity of M. grisea were reported in this paper, The prospects of the application of the techniques were discussed as well.