Candida kruseiis aCandidanon-albicans species with a high prevalence, which causes candidaemia. Current treatment guidelines include fluconazole as a primary therapeutic option for the treatment of these infections; however, it is only a fungistatic againstCandida spp., and both inherent and acquired resistance to fluconazole have been reported.C.kruseispecies is also reported as the onlyCandida sp. which has an intrinsic resistance factor to fluconazole. Therefore, in dealing with antifungal resistance, it is necessary to develop new antifungal agents that are efficient in the treatment of fungal infections, especially those caused byC. krusei. The purpose of this study was to investigate the genome of clinicalC. kruseiisolates and correlate the resistant phenotypes with mutations in resistance genes. A total of 16 samples ofC. kruseifrom clinical samples from hospitals in Jakarta were used in the experiment. All colonies were extracted using the QIAamp DNA Mini Kit. The library was prepared using the Illumina DNA Prep Kit. The sequencing process was carried out on the Illumina MiSeq Platform using a 2x301 paired-end configuration. FASTQ raw files are available under the BioProject Accession Number PRJNA819536 and Sequence Read Archive Accession Numbers SRR18739949 and SRR18739964.