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<i>Aspergillus flavus</i>, a ubiquitous filamentous fungus found in soil, plants and other substrates has been reported not only as a pathogen for plants, but also a carcinogen producing fungus for human. Peptidyl-Prolyl Isomerase (PPIases) plays an important role in cell process such as protein secretion cell cycle control and RNA processing. However, the function of PPIase has not yet been identified in <i>A. flavus.</i> In this study, the PPIases gene from <i>A. flavus</i> named <i>ppci1</i> was cloned into expression vector and the protein was expressed in prokaryotic expression system. Activity of recombinant ppci1 protein was particularly inhibited by FK506, CsA and rapamycin. 3D-Homology model of ppci1 has been constructed with the template, based on 59.7% amino acid similarity. The homologous recombination method was used to construct the single <i>ppci1</i> gene deletion strain Δ<i>ppci1</i>. We found that, the <i>ppci1</i> gene plays important roles in <i>A. flavus</i> growth, conidiation, and sclerotia formation, all of which showed reduction in Δppci1 and increased in conidiation compared with the wild-type and complementary strains in <i>A. flavus.</i> Furthermore, aflatoxin and peanut seeds infection assays indicated that <i>ppci1</i> contributes to virulence of <i>A. flavus.</i> Furthermore, we evaluated the effect of PPIase inhibitors on <i>A. flavus</i> growth, whereby these were used to treat wild-type strains. We found that the growths were inhibited under every inhibitor. All, these results may provide valuable information for designing inhibitors in the controlling infections of <i>A. flavus</i>.