Fungal aetiology of keratitis/corneal ulcer is considered to be one of the leading causes of ocular morbidity, particularly in developing countries including India. More importantly,FusariumandAspergillusare reported commonly implicating corneal ulcer and against this background the present work was undertaken so as to understand the current epidemiological trend of the two fungal keratitis. During the project period, a total of 500 corneal scrapings were collected from suspected mycotic keratitis patients, of which 411 (82.2%) were culture positive for bacteria, fungi, and parasites. Among fungal aetiologies,Fusarium(216, 52.5% of 411) andAspergillus(68, 16.5% of 411) were predominantly determined. While the study revealed a male preponderance with both the fungal keratitis , it further brought out that polyene compounds (natamycin and amphotericin B) and azoles were active, respectively, againstFusariumspp. andAspergillusspp. Additionally, 94.1% of culture provenFusariumkeratitis and, respectively, 100% and 63.6% ofA. flavusandA. fumigatuswere confirmed by multiplex PCR. The sensitivity of the PCR employed in the present study was noted to be 10 fg/μl, 1 pg/μl, and 300 pg/μl of DNA, respectively, forFusarium,A. flavus,andA. fumigatus.Alarming fact was thatFusariumandAspergillusregionally remained to be the common cause of mycotic keratitis and theFusariumisolates had a higher antifungal resistance thanAspergillusstrains against most of the test drugs.