: Since first isolate of Candida (C.) auris was recognized in 2018 in China, over 60 cases of C. auris colonization or infection have been reported up to 2022, with at least two distinct genetic clade. Most isolates from South Asian clade and South African clade were sensitive and resistant to fluconazole, respectively. Here, we report an isolate of fluconazole-resistant South Asian clade C. auris (PUSH159) from blood. The efflux pump genes MDR1, CDR1, CDR4, SNQ2, and ARB1, and ergosterol biosynthesis gene ERG11 were detected in strain PUSH159. Single nucleotide polymorphism (SNP) analysis revealed that strain PUSH159 carried multiple mutations in drug resistance-associated genes, including a hot-spot mutation (Y132F) in ERG11, missense mutation of E709D in CDR1, and missense mutations of K52N and E464K in SNQ2. Our findings support the genetic diversity and differences in antifungal susceptibility within the South Asian clade, and provide early warning for the emergence of fluconazole-resistant South Asian clade isolates in China.