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The parasites from buffaloes in Guizhou province, southwest China, were suspected to be sarcocysts through morphologic observation. 18S rRNA and the subunit I of cytochrome oxidase (cox1) sequences were amplified, then implemented by phylogenetic analysis. Phylogenetic analyses of 18S rRNA and cox1 genes both indicated the low degree of genetic diversity among the isolated sequences and other sequences of Sarcocystis fusiformis. The result shows that the sarcocysts from these buffaloes in Guizhou province S. fusiformis. This study is the first molecular characterization of S. fusiformis from Chinese buffaloes that used two genetic markers (18S rRNA and cox1 sequences) in China.