The main aim of present study is to ascertain the fungal species and their effect on germination associated with wheat seeds. Seeds of three varieties WH896, PBW-373 and HD264 of wheat (Triticum aestivum) were collected from Quarsi Agriculture Farm Aligarh. These three seed samples of wheat showing different forms of discouloration and abnormalities were screened for associated fungi. Microscopic examination of wheat seeds reveals that seeds of all the varieties of wheat possess injuries to varying extent. Detailed examination of the seeds has shown that the seeds can be classified on the basis of extent of injury in the three categories viz., seeds having minor cracks, cracks without exposed embryo and cracks with exposed embryo. Seed soaking and washing techniques were also employed. Fusarium moniliforme and Alternaria alternata were isolated from all the categories of seed tested. Floating mycelial bits and conidia of Alternaria, Fusarium, Drechslera, Curvularia lunata, Mucor were found in all the three varieties of wheat. The seeds were subjected to visual observation and examination under stereoscopic microscope. These findings are to study and detect the phytopathogenic mycoflora which causes damage and loss to our seeds and crops.