This study reports the first whole-genome sequencing (WGS) analysis of *Candida auris* isolates from Bangladesh, identifying a novel sixth clade (Clade VI) of the fungus. The research involved 10 *C. auris* isolates collected from hospital settings, which were initially identified using CHROMagar Candida Plus and VITEK2 systems. WGS analysis revealed that all isolates aligned closely with Clade I, with 8 out of 10 isolates clustering with Clade I isolates, indicating a South Asian lineage prevalent in Bangladesh. However, two isolates formed a distinct cluster with >42,447 single-nucleotide polymorphism (SNP) differences compared to their closest Clade IV counterparts, confirming the emergence of Clade VI. Antifungal susceptibility testing (AFST) showed that 80% of the isolates were resistant to fluconazole and voriconazole, while Clade VI isolates were susceptible to azoles, echinocandins, and pyrimidine analogs. Genomic sequencing identified the ERG11_Y132F mutation as conferring azole resistance, while the FCY1_S70R mutation was inconsequential in describing 5-flucytosine resistance. The study underscores the need for comprehensive genomic surveillance in Bangladesh to better understand the emergence, transmission dynamics, and resistance profiles of *C. auris* infections. The discovery of Clade VI highlights the importance of advanced sequencing methodologies in uncovering new fungal lineages.This study reports the first whole-genome sequencing (WGS) analysis of *Candida auris* isolates from Bangladesh, identifying a novel sixth clade (Clade VI) of the fungus. The research involved 10 *C. auris* isolates collected from hospital settings, which were initially identified using CHROMagar Candida Plus and VITEK2 systems. WGS analysis revealed that all isolates aligned closely with Clade I, with 8 out of 10 isolates clustering with Clade I isolates, indicating a South Asian lineage prevalent in Bangladesh. However, two isolates formed a distinct cluster with >42,447 single-nucleotide polymorphism (SNP) differences compared to their closest Clade IV counterparts, confirming the emergence of Clade VI. Antifungal susceptibility testing (AFST) showed that 80% of the isolates were resistant to fluconazole and voriconazole, while Clade VI isolates were susceptible to azoles, echinocandins, and pyrimidine analogs. Genomic sequencing identified the ERG11_Y132F mutation as conferring azole resistance, while the FCY1_S70R mutation was inconsequential in describing 5-flucytosine resistance. The study underscores the need for comprehensive genomic surveillance in Bangladesh to better understand the emergence, transmission dynamics, and resistance profiles of *C. auris* infections. The discovery of Clade VI highlights the importance of advanced sequencing methodologies in uncovering new fungal lineages.