Endophytic fungi are widely known as fungi that infect internal tissues of host plants for all or part of their life cycles, without causing visible symptoms of disease. The present study was carried out to identify and investigate the pathogenicity of endophytic fungi residing in husks, silks, and kernels of corn. Endophytic fungi were isolated from surface-sterilised silks, kernels, and husks of healthy corn plants and identified using sequencing of multiple markers comprising TEF-1α, β-tubulin, calmodulin, ITS, LSU, and ACT. A total of 56 isolates of endophytic fungi belonging to 17 species, namely Fusarium pseudocircinatum (n = 8), F. verticillioides (n = 2), F. andiyazi (n = 4), F. sacchari (n = 1), F. mangiferae (n = 1), F. fujikuroi (n = 1), F. proliferatum (n = 3), F. incarnatum (n = 2), Penicillium oxalicum (n = 2), P. polonicum (n = 2), P. citrinum (n = 11), Aspergillus flavus (n = 10), A. tubingensis (n = 1), Cladosporium tenuissimum (n = 3), Aureobasidium pullulans (n = 3), Curvularia lunata (n = 1), and Epicoccum sorghinum (n = 1) were identified. Pathogenicity test showed that all endophytic fungi induced varying severities of disease symptoms on corn plants such as leaf chlorosis and necrosis, stem malformation, wilt, and stunted growth with F. verticillioides being the most virulent. The study revealed that corn tissues harbour diverse genera of endophytic fungi that can infect corn plants and may cause harmful effects to the host plants.