Rice blast caused by Magnaporthe oryzae(M.oryzae) is one of the most destructive diseases,which causes significant rice yield losses and affects global food security.To better understand genetic variations among different isolates of M.oryzae in nature,we re-sequenced the genomes of two field isolates,CH43 and Zhong-10-8-14,which showed distinct pathogenecity on most of the rice cultivars.Genome-wide genetic variation analysis reveals that ZHONG-10-8-14 exhibits higher sequence variations than CH43.Structural variations(SVs) detection shows that the sequence variations primarily occur in exons and intergenic regions.Bioinformatics analysis for gene variations reveals that many pathogenecity-related pathways are enriched.In addition,193 candidate effectors with various DNA polymorphisms were identified,including two known effectors AVR-Pik and AVR-Pital.Comparative polymorphism analysis of thirteen randomly selected effectors suggests that the genetic variations of effectors are under positive selection.The expression pattern analysis of several pathogenecity-related variant genes indicates that these genes are differentially regulated in two isolates,with much higher expression levels in Zhong-10-8-14 than CH43.Our data demonstrate that the genetic variations of effectors and pathogenecity-related genes are under positive selection,resulting in the distinct pathogenicities of CH43 and Zhong-10-8-14 on rice. Rice blast caused by Magnaporthe oryzae (M. oryzae) is one of the most destructive diseases, which causes significant rice yield losses and affects global food security.To better understand genetic variations among different isolates of M. oryzae in nature, we re-sequenced the genomes of two field isolates, CH43 and Zhong-10-8-14, which showed distinct pathogenecity on most of the rice cultivars. Genome-wide genetic variation analysis reveals that ZHONG-10-8-14 exhibits higher sequence variations than CH43. Structural variations (SVs) detection shows that the sequence variations occur occur in exons and intergenic regions. Bioinformatics analysis for gene variations reveals that many pathogenecity-related pathways are enriched. In addition, 193 candidate effectors with various DNA polymorphisms were identified, including two known effectors AVR-Pik and AVR-Pital. Comparative polymorphism analysis of thirteen randomly selected effectors suggests that the genetic variations of effectors are under p ositive selection. The expression pattern analysis of several pathogenecity-related variant genes that those genes are differentially regulated in two isolates, with much higher expression levels in Zhong-10-8-14 than CH43. Our data demonstrate that the genetic variations of effectors and pathogenecity-related genes are under selection, resulting in the distinct pathogenicities of CH43 and Zhong-10-8-14 on rice.