A total of 70 feathers samples of Emu (Dromaius novaehollandiae) were collected from 7 Emu farms situated at two districts (Raigad and Thane) of Maharashtra (India) and screened for resident keratinophilic fungi. Among them, 44 isolates were recovered and identified by evaluating characteristic macro- and micro-morphological features. Further gene products corresponding to the ITS1-5.8S-ITS2 rDNA region from all isolates were amplified and sequenced. Homology search was performed using BLAST program against non-redundant nucleotide database, and significantly matched DNA sequences deposited to the NCBI Gene Bank for reference purposes. Eight identified fungal species belongs to 7 different genera named as Aphanoascus terreus Ac_MW577456 (21.43%), Microsporum gypseum Ac_MW580920 (14.29%), Ctenomyces serratus Ac_MW577459 (10.0%), Uncinocarpus orissi Ac_MW577461 (5.17%), Aphanoascus verrucosus Ac_MW577458 (4.29%), Gymnascella dankaliensis Ac_MW577460 (2.86%), Gymnoascoideus petalosporus Ac_MW577462 (2.86%) and Arthroderma tuberculatum Ac_MW577457 (1.43%).