A total of 130 maize and sorghum samples from 15 districts of Karnataka state were analyzed for diversity and per cent incidence of Fusarium species by direct plating method on malachite green agar 2.5 medium. For further identification of Fusarium species, one set of genus-specific ITS primers was used to differentiate Fusarium species from closely related genera by polymerase chain reaction. The study revealed the occurrence of 10 diverse species of Fusarium in maize and sorghum samples collected from different districts of Karnataka. The species identified were F. verticillioides, F. proliferatum, F. oxysporum, F. anthophilum, F. pallidoroseum, F. sporotrichioides, F. solani, F. graminearum, F. decemcellulare, and F. lateritium respectively. All the Fusarium species tested by PCR scored positive with the ITS pair of primers with an expected 431bp PCR product. The study further revealed the occurrence of F. verticillioides (18.69%), F. proliferatum (6.08%), and F. anthophilum (4.46%) in maize samples respectively. Similarly, species of F. verticillioides (10.22%) and F. anthophilum (1.67%) were recorded in higher per cent incidence in sorghum samples. The data on the diversity and incidence of Fusarium species would be of great significance for predicting the extent of post-harvest deterioration and subsequent accumulation of toxins in maize and sorghum grains produced in Karnataka, India.