Rhodotorula mucilaginosa rarely cause keratitis in immunocompromised individuals. A 30 year old male with history of minor trauma presented with cotton wool like stromal infiltration and hypopyon in left eye. Microbiological examination of corneal scraping showed fungal hyphae and yeast cells in direct smear. Molecular identification of the organism was performed which showed 100% homology with Rhodotorula mucilaginosa. Management of these cases is difficult often necessitating surgical procedures. However further reports are necessary to understand the disease and establish a treatment protocol.