Keratinophilic fungi are ecologically and epidemiologically significant group of fungi that cycle one of the most abundant and highly stable animal proteins on earth - keratin. Keratinophilic fungi exemplify a vast biodiversity of form, habitat and substrates. However, studies are rather meager in wetland agroecosystems and the present work has been undertaken to record the presence of keratinophilic fungi in a wetland agroecosystem in Kerala, India. Altogether, a total of 38 species of fungi comprising 22 genera were identified from the 120 soil samples collected from different areas of oil palm agricultural fields in the wetland agroecosystem from July 2015 to July 2016. A total of 11 fungi were recorded throughout the study irrespective of seasons. North East monsoon season fetched more fungi (30 species) followed by early summer (29 species), late summer (19 species) and south west monsoon season (18 species). It is clear from the results that soils of Vembanadu wetland agroecosystem provides ideal environment for the growth of keratinophilic fungi and dermatophytes which is be attributed to the high organic debris and keratinous substrates like rodent hair and feathers from birds and other animals and plant litter present in these soils. Thus the presence of these fungi which are human and animal pathogens are considered as bioindicators of environmental pollution with keratinous substrate which can pose risk of human and animal mycoses in the region.