Chelatococcus daeguensis strain M38T9 is a thermotolerant bacterium isolated from a hot-spring in Malaysia. The draft genome of C. daeguensis strain M38T9 consists of 4,218,658 bp assembled into 50 scaffolds. The GC content of the genome is 67.91 %, and the sequencing coverage of 184×. There are 4,046 predicted genes, 3,962 protein-coding genes, and 53 RNA-coding genes (tRNA: 45, rRNA: 4). The draft genome has been deposited at DDBJ/ENA/GenBank under the BioProject accession number PRJNA668056. The raw reads were deposited in the Sequence Read Archive (SRA) under accession number SRR13805582. Here we report the draft genome of this strain to expand our understanding of the genomic information available on the genus Chelatococcus.