<p class="abstract"><strong>Background:</strong> Chronic otitis media (COM) is commonly encountered chronic inflammation of the middle ear cleft caused by dysfunction of Eustachian tube followed by microbial infection. Fungal infections superimposed over COM are suspected when the discharging ear does not respond to the local antibiotic ear drops. Many authors have focused their attention on the bacterial flora of COM but very little is known about the mycological aspects.</p><p class="abstract"><strong>Methods:</strong> Ear discharge or scrapings of debris were collected from one hundred patients of active mucosal COM in whom discharge persists after two weeks of medical management and sent to the microbiology laboratory for microscopic examination and fungal culture. </p><p class="abstract"><strong>Results:</strong> Fifty seven percent cases had positive fungal KOH mount whereas fungal culture demonstrated Aspergillus flavus in 15 cases, Aspergillus niger in 38 cases and Candida albicans in 4 cases. </p><p class="abstract"><strong>Conclusions:</strong> We conclude that the fungal isolation rate is very high among the patients who did not respond to antibiotic therapy and therefore, culture and sensitivity of discharge and removal of the focus of infection should be sought before using topical drops in cases of persistent otorrhoea.</p>