In this study, nine maize varieties (NAH-1137, CM-500, NAC-6004, Nithyashree, Seed tech-2324, Bio-9637, Bio-9681, DHM117 and COH(M)10) plants were grown at NBAIR farm, Bangalore, India, from January 2015 to April 2015. A total of 17 fungal endophytes isolated from leaf, stem and root fragments collected about thirty, sixty and ninety days after seeds sown. The fungi were identified as Acremonium zeae, Cladosporium oxysporum, Colletotrichum boninense, Colletotrichum gloeosporioides, Coprinopsis cinerea, Curvularia lunata, Epicoccum sorghinum, Fusarium fujikuroi, Gibberella moniliformis, Nemania sp., Penicillium sp., Rigidoporus vinctus, Sarocladium zeae and Scopulariopsis gracilis. Difference was found in the number of fungi isolated from leaves, stems and roots irrespective of maize varieties. Presence of fungal endophytes were more in leafs than stems and roots of maize.  Irrespective of maize tissues, more fungi were isolated about sixty days after seeds sown. The isolate Furarium fujikuroi showed higher colonization with 34.02%, followed by the genera Penicillium with 17.01% colonization. Furthermore, fungal endophytes were evaluated for their pathogenicity against C. partellus, among the endophytes tested Cladosporium oxysporum and Rigidoporus vinctus isolates showed 6.67 and 10% mortality respectively.