Debaryomyces hansenii J6 is a heavy metal tolerant, flavinogenic marine yeast strain isolated from a Swedish estuary. Here we report the 11.55 Mb genome of this organism that contains 5,718 open reading frames open reading frames. Genomic comparison with currently available Debaryomyces spp. genomes was performed in this study. Several Next Generation Sequencing mapping aligner tools were applied to determine genomic homology of J6 with D.hansenii MTCC 234, D.fabryi CBS7 89, and D.hansenii CBS 767. Our results demonstrate that J6 is closer to MTCC 234 (95%) than D. fabry CBS 789 and D. hansenii</p><p>CBS 767.