Aplastic anemia is defined by profound reduction in number of bone marrow- Hematopoietic stem cell or Hematopoietic progenitor cell. Fungal infection is the second cause of infections caused in hematopoietic stem cell transplant patients, with viral infection being first and bacterial accounts third. Candida duobushaemulonii is an emerging pathogen, given its resistance to multiple antifungal (to azoles and amphotericin B) it poses a substantial problem of causing invasive infection in immunocompromised setting. The Candida duobushaemulonii requires molecular based method for accurate identification and the conventional/ traditional biochemical method is currently inadequate. Trichosporon asahii is one of the most common species of trichosporon genus, which is a rare fatal emerging fungal infection whose occurrence has increased in immunocompromised patients with blood disease. A 58-year-old patient was diagnosed to have very severe aplastic anemia and febrile neutropenia post stem cell transplant.On basis of Sputum analysis the patient was diagnosed to have aspergillus pneumonia with High resolution computed tomography showing moderate pleural effusion and blood and urine culture revealed presence of fungal infections for which he was then started on antibiotics and antifungal. Blood Culture revealed that Candida duobushaemulonii was resistant to fluconazole and voriconazole and had a good sensitivity to echinocandins hence the patient was started on inj Anidulafungin 100 mg OD for 12 days. After 3 days the patient became hypoxic, required 2 litres of oxygen through face mask to maintain saturation, the urine and blood culture were sent in which urine culture reports showed Trichosporon asahii which was then treated with inj Anidulafungin 100 mg after which the patient was stable and afebrile. Echinocandins are more susceptible to Candida duobushaemulonii whereas azoles and amphotericin B are resistant. EarlyAnalysis of the risk factor to develop Candida duobushaemulonii and Trichosporon asahii priorto stem cell transplant is required and possibly will help in identifying this rare fungal infection by using molecular method rather than by using a traditional method and it also helps in choosing a better prophylactic antifungal.