The proteomic amino acids of Toxoplasma gondii strains GT1, ME49 and VEG, Plasmodium, and 44 other eukaryote species were downloaded from related databases. The amino acid sequences of various T. gondii strains and other species were searched using the HMMER3 software to identify the phosphatases of. T. gondii and other species. Cluster analysis was performed for all of the identified phosphatases to extract the conserved amino acid sequences of phosphatases, and phylogenetic trees were constructed with the neighbor-joining method and maximum likelihood method, respectively. Meanwhile, the catalytic domains of these identified phosphatases were annotated using the Pfam online tool, and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Gene array data were used to analyze and compare the transcription levels of protein phosphatases in different strains and at different developmental stages of ME49 strain. Results showed that 64 phosphatases were identified, which were classified into 5 subfamilies: phosphoprotein phosphatase (PPP) family (11 proteins), protein tyrosine phosphatase-like A (PTPLA) family (1 protein), ASP-dependent tyrosine phosphatase (APP) family (8 proteins), dual-specificity phosphatase (DSP) family (9 proteins) and Mg ²⁺ or Mn ²⁺-dependent protein phosphatase (PPM) family (35 proteins). The bioinformatics analysis revealed that the identified phosphatases mainly possessed phosphatase activity, hydrolase activity and catalytic activity, and participated in the regulation of dephosphorylation. The phylogenetic analysis suggested that the phosphatases were conserved among the T. gondii strains. In addition, similar protein phosphatase expression profiles were found at the tachyzoite stage of different T. gondii strains. The most significant difference was found in TG_312200 among different stains. Its expression in ME49 was 4 times as that in the GT1 strain and VEG strains. However, the transcription levels of some phosphatases varied significantly among various developmental stages of the ME49 strain. For example, TG_318660 transcription was at a low level in unsporulated oocysts while TG_304955 transcription was at a high level in both tachyzoites and bradyzoites. These results suggested that these differentially expressed phosphatases may play essential roles in the development of T. gondii.