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With only four classes of antifungal drugs available for the treatment of invasive systemic fungal infections, the number of resistant fungi is increasing, highlighting the urgent need for novel antifungal drugs. Ergosterol, an essential component of cell membranes, and its synthetic pathway have been targeted for antifungal drug development. Sterol-C4-methyl monooxygenase (Erg25p), which is a greater essential target than that of existing drugs, represents a promising drug target. However, the development of antifungal drugs must consider potential side effects, emphasizing the importance of evaluating their selective toxicity against fungi. In this study, we knocked in <i>ERG25</i> of <i>Candida glabrata</i> and its human ortholog, <i>SC4MOL</i>, in <i>ERG25</i>-deleted <i>Saccharomyces cerevisiae</i>. Utilizing these strains, we evaluated 1181-0519, an Erg25p inhibitor, that exhibited selective toxicity against the <i>C. glabrata ERG25</i> knock-in strain. Furthermore, 1181-0519 demonstrated broad-spectrum antifungal activity against pathogenic <i>Candida</i> species, including <i>Candida auris</i>. The approach of utilizing a gene that is functionally conserved between yeast and humans and subsequently screening for molecular target drugs enables the identification of selective inhibitors for both species.