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Mycotoxins are secondary metabolites produced by different fungus species which are harmful both for the animals and human beings. In this study, feed samples were taken from different livestock farms and commercial feed mills and levels of aflatoxin B1 and prevalence of Aspergillus species in each sample was recorded. The anti-fungal potential of different plant extracts was also evaluated. The aflatoxin B1 was measured by HPLC. Results showed Aflatoxin B1 was most prevalent in feed collected from the farms as compared to commercial feed mills. Six genera of fungus were found and 14 species of these six genera were identified. Comparative efficacy of methanolic extracts of garlic (Allium sativum L.), clove (Syzygium aromaticum) and neem (Azadirachta indica) were determined by agar well diffusion method. Garlic (Allium sativum L.) showed significantly higher antifungal activity followed by clove (Syzygium aromaticum) and neem (Azadirachta indica) at (P<0.05).