Candida auris is an emerging yeast pathogen with a remarkable ability to develop antifungal resistance, in particular to fluconazole and other azoles. Azole resistance in C. auris was shown to result from different mechanisms, such as mutations in the target gene ERG11 or gain-of-function (GOF) mutations in the transcription factor TAC1b and overexpression of the drug transporter Cdr1. The roles of the transcription factor Mrr1 and of the drug transporter Mdr1 in azole resistance is still unclear. Previous works showed that deletion of MRR1 or MDR1 had no or little impact on azole susceptibility of C. auris. However, an amino acid substitution in Mrr1 (N647T) was identified in most C. auris isolates of clade III that were fluconazole resistant. This study aimed at investigating the role of the transcription factor Mrr1 in azole resistance of C. auris. While the MRR1 ^N647T mutation was always concomitant to hot spot ERG11 mutations, MRR1 deletion in one of these isolates only resulted in a modest decrease of azole MICs. However, introduction of the MRR1 ^N647T mutation in an azole-susceptible C. auris isolate from another clade with wild-type MRR1 and ERG11 alleles resulted in significant increase of fluconazole and voriconazole MICs. We demonstrated that this MRR1 mutation resulted in reduced azole susceptibility via upregulation of the drug transporter MDR1 and not CDR1. In conclusion, this work demonstrates that the Mrr1-Mdr1 axis may contribute to C. auris azole resistance by mechanisms that are independent from ERG11 mutations and from CDR1 upregulation.