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We explored the composition and roles of the protein phosphatase 2C (<i>PP2C</i>) family in <i>Paulownia fortunei</i>. The genome <i>P. fortunei</i> harbored 91 <i>PfPP2C</i> genes, encoding proteins with 120–1107 amino acids (molecular weight range, 13.51–124.81 kDa). The 91 <i>PfPP2Cs</i> were distributed in 12 subfamilies, with 1–15 <i>PfPP2C</i>s per subfamily. The number and types of conserved structure domains differed among <i>PP2Cs</i>, but the distribution of conserved motifs within each subfamily was similar, with the main motif structure being motifs 3, 16, 13, 10, 2, 6, 12, 4, 14, 1, 18, and 8. The <i>PfPP2C</i> genes had 2 to 20 exons. There were ABA-response elements in the promoters of 42 <i>PfPP2C</i> genes, response elements to phytohormones, and stress in the promoters of other <i>PfPP2C</i> genes. A covariance analysis revealed that gene fragment duplication has played an important role in the evolution of the <i>PfPP2C</i> family. There were significant differences in the transcript levels of some <i>PfPP2C</i> genes in <i>P. fortunei</i> affected by witches’ broom (PaWB) and after treatment with rifampicin and methyl methanesulfonate. <i>PfPP2C02</i>, <i>PfPP2C12</i>, <i>PfPP2C19</i>, and <i>PfPP2C80</i> were strongly related to PaWB. These findings provide a foundation for further studies on the roles of <i>PP2C</i>s in PaWB.