Background: The apicomplexan protozoan parasite Toxoplasma gondii is one of the most successful intracellular parasites capable of infecting warm-blooded animals. Several strains of T. gondii have been described and typed as virulent or avirulent based on their pathogenicity in mice, as well as sporulated oocysts of strains belonging to distinct T. gondii genotypes. Phosphorylation is a reversable form of protein post-translational modification (PTM) that influences many biological processes and is used by some apicomplexan parasites to facilitate manipulation of the host cells. Phosphoproteomic analysis of oocysts of T. gondii strains belonging to distinct genotypes may reveal mechanisms contributing to the differences in the virulence of this parasite at the posttranslational level.Methods: In this study, the differences in the phosphoproteomic landscape of sporulated oocysts between virulent and avirulent strains of Toxoplasma gondii were examined using a global phosphoproteomics approach. Phosphopeptides from sporulated oocysts of the virulent PYS strain (Chinese ToxoDB#9) and the avirulent PRU strain (type II) were enriched by titanium dioxide (TiO2) affinity chromatography and quantified using isobaric tag (iBT) approach. Motif analysis, GO enrichment, KEGG pathway analysis, STRING analysis and kinase related network analysis of phosphopeptides were conducted to discover distinct difference in sporulated oocysts between virulent and avirulent T. gondii strains. Results: A total of 10,645 unique phosphopeptides, 8,181 nonredundant phosphorylation sites and 2,792 phosphoproteins were identified. We also detected 4,129 differentially expressed phosphopeptides (DEPs) between sporulated oocysts of PYS strain and PRU strain (|log1.5 fold change| > 1 and p < 0.05), including 2,485 upregulated and 1,644 downregulated phosphopeptides. Motif analysis identified 24 motifs from the upregulated phosphorylated peptides including 22 serine motifs and two threonine motifs (TPE and TP), and 15 motifs from the downregulated phosphorylated peptides including 12 serine motifs and three threonine motifs (TP, RxxT and KxxT) in PYS strain when comparing PYS strain to PRU strain. Several kinases were consistent with motifs of overrepresented phosphopeptides, such as PKA, PKG, CKII, IKK, MAPK, EGFR, INSR, Jak, Syk, Src, Ab1. GO enrichment, KEGG pathway analysis and STRING analysis revealed DEPs significantly enriched in many biological processes and pathways. Kinase related network analysis showed that AGC kinase had the greatest connected peptides.Conclusions: The present study revealed the global phosphoproteomic differences in sporulated oocysts between virulent and avirulent T. gondii strains of different genotypes. Abundant phosphopeptides in sporulated oocysts between virulent and avirulent T. gondii strains exhibited distinct difference in the conserved motifs, GO terms, enriched pathways and PPI networks. The kinase associated network analysis indicated the role of phosphorylation in the transformation of T. gondii kinases. AGC kinase was the most connected kinases peptides. These data provide new insight into the phenotypic differences in sporulated oocysts of virulent and avirulent T. gondii strains.