Understanding of protein expression difference in the same stage of T.gondii among different genotypes will facilitate the elucidation of genotypic divergence among the T.gondii strains. A 4-plex iTRAQ (isobaric tag for relative and absolute quantitation) based LC-MS/MS approach was employed to survey the differentially expressed proteins of sporulated oocysts between ToxoDB#1 (PRU) strain and ToxoDB#9 (PYS) strain for the first time.