This study aimed to explore the incidence of Fusarium fungi and their mycotoxins in marketed feed in Qatar. Samples of mixed-grain-cereal, maize, wheat, millet, barley, oat and soybean were tested for the presence of zearalenone (ZEN), fumonisins, T2/HT2 and deoxynevalenol (DON) mycotoxins. PCR-based identification of the Fusarium isolates was followed by investigation into genes involved in trichothecenes (tri gene cluster), fumonisins (fum gene cluster) and ZEN (pks gene) biosynthesis. In-vitro mycotoxin production potential of the isolates was compared with their molecular profiles. Mixed-grain cereals showed highest contamination with Fusarium, followed by maize and wheat. The incidence of ZEN was highest in mixed grain samples (87.5%) followed by maize (50%), millet (42.85%) and wheat (40%). In case of DON; 62.5%, 30%, 40%, 14.28%, 50% and 66.67% of the tested mixed cereal grain, maize, wheat, millet, barley and soybean samples were positive. Based on PCR results, F. verticillioides showed highest frequency distribution (34%), followed by F. graminearum (16%), F. oxysporum (15%), F. proliferatum (13%), F. culmorum (8%), F. solani (7%), F. subglutinans (4%) and F. avenaceum (3%) in the feed cereals. All the isolates of F. verticillioides presented both fum1 and fum13 genes, and produced fumonisin mycotoxins in-vitro. All the isolates of F. graminearum and F. culmorum had the tri5 and tri6 genes and resulted in DON accumulation in rice media. In addition to DON, all the F. culmorum isolates produced ZEN in artificially contaminated media, in line with their molecular profile of having tri5, tri6 and pks13 genes. The findings of present study confirmed the occurrence of toxigenic Fusarium and their mycotoxins in animal feed, all below the maximum limit set by EU. Further, the in-vitro mycotoxin production potential of the isolates was in agreement with their tri, fum and pks genetic profiles.