Carotenoids are valuable pigments that have been widely used in food, pharmaceutical, animal breeding and cosmetics industries. Due to the increasing demand for carotenoids of natural origin, the trend for production of carotenoids by red yeast has become popular. Strain Rhodotorula mucilaginosa CYJ03 was isolated from northern Yellow Sea of China for its carotenoid producing potential. It was found that the whole genome of CYJ03 was 19.03 Mb in size and contained 6301 protein-coding genes including a gene cluster for the carotenoids biosynthesis. The genome sequence would be valuable for exploring the potential biological properties of CYJ03, as well as for facilitating the molecular genetic analysis and the manipulation of carotenoids accumulation in this strain, and for the development of it as an engineered host for carotenoid production.