We have found the Ndt80p transcription factor involved in drug resistance by positively regulating ef?ux pump CDR1 in Candida albicans, the most common human fungal pathogens for systemic infection. When investigating its target genes, we have found that the expression of YHB1 is affected by Ndt80p. Hence, we are interested in understanding the involvement of Ndt80p in the stress responses of C. albicans. We have applied genetic and functional studies to characterize the cellular functions of Ndt80p as well as site-directed mutagenesis to identify the potential Ndt80p binding sites on the target genes. We found that Ndt80p directly regulated its target genes, such as YHB1, via the mid-sporulation element (MSE). The direct interaction between Ndt80p and the MSE site was demonstrated by electrophoretic mobility shift assays (EMSA). We further found that the ndt80 R432A allele, with a reduced capability to bind MSE, failed to complement the defects caused by null mutations of NDT80. In fact, the R432 residue in the Ndt80p DNA-binding domain was involved in several tested functions, including drug resistance, nitric oxide inactivation, germ tube formation, hyphal growth, and virulence. In conclusion, Ndt80p is an important transcription modulator to various stress-response genes in C. albicans. In addition, the importance of the R432 residue suggests a novel approach to design new antifungal drugs through screening compounds blocking the interaction between Ndt80p and its targets.