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Contamination of livestock feed is a serious problem worldwide during storage. Fungal infection reduces nutritional quality of feed and affects the animal health, thus reducing the livestock profitability. The aim of this study was to investigate the mycoflora of 73 samples representing four raw cereals; (corn, barley, soybean and wheat bran) and three concentrate finished feed of (dairy cow, poultry and pellet). Isolation of internal and external mycoflora was carried out using dilution plate and direct plate methods. The result of the dilution technique revealed that Aspergillus, Penicillium, Fusarium and Alternaria were the most frequently occurring genera. The analyzed samples showed fungal contamination ranging from 18.84 × 103 CFU/g to 55.23 × 103 CFU/g. Comparing the different feed types, finished concentrates had greater fungal contamination compared to the raw ingredients. The most directed external mycoflora in corn, barley and soybean, using the direct plate technique were Aspergillus (100%, 85.66%, 75%) and Penicillium (83.33%, 50%, 50%) respectively. However, Atlernaria (83.33%, 57% and 75%) and Fusarium (66.33%, 71.33% and 50%) were the most predominant internal mycoflora genera. The overall percentage of fungal infection was higher in non-surface disinfected seeds compared to surface disinfected ones. Fungal infection affected quality of grain through reduction in germination. It seems that livestock feed is highly affected by fungi and special storage and conditioning are required to reduce the fungal infection and protect the animal and human health.