Mycotoxins are toxic secondary metabolites produced by Fusarium species. The most prevalent Fusarium-species in feedstuffs produced in Karnataka, India is Fusarium verticillioides. Little is known about the diversity of Fusarium species and occurrence of fumonisin levels. This study was conducted to detect and assess the significance of Fusarium species as natural contaminants. A total of 200 animal feedstuffs and poultry feed mixtures were analyzed for per cent incidence, diversity and frequency of Fusarium species by serial dilution and agar plating method. The study revealed the occurrence of nine diverse species of Fusarium. Manual identification of Fusarium species was confirmed with molecular detection by PCR method using genus specific primers. The toxigenic potential of potential fumonisin- producing strains was also determined using genus-specific and species-specific primer sequences. The analytical method namely High Performance Liquid Chromatographic technique was applied to Indian animal feedstuffs and poultry feed mixtures, to establish the fumonisin levels. The study warranted the need for proper surveillance and monitoring of contaminated feeds.