The genome of A. fumigatus contains ~9900 genes, but few antifungal targets have been developed yet. In the present study, we compared the whole proteome of A. fumigatus with Saccharomyces cerevisiae, as a non-pathogen fungal organism, to identify Aspergillus-specific proteins. Amongst the proteins, those with close homologues to human were removed, and the final targets were selected. One novel target, the aspergillus fumigatus RNA-binding protein (AfuRBP), was selected and found to be a peptidylprolyl isomerase (PPI). For further functional studies, AfuRbp knock out and knock down mutant strains were generated. MIC assay with known inhibitors, phenylglyoxal and juglone, and a synthetic derivative of juglone confirmed the higher sensitivity of the mutants to these compounds when compared to the wild-type strain.