Pearl millet (Pennisetum glaucum) or Bajra is one of the important cereal crops of Africa and India, though it is used throughout the world as nutritious and gluten-free diet. Pearl millet grains/seeds are known to carry several pathogenic and non-pathogenic fungi which alter physio-chemical properties of the seeds, losses of the seed weight, germination potential, and deterioration of quality. During present investigation, 150 seed samples were collected from 15 Tehsils of major pearl millet growing districts of Rajasthan. Ten samples of each Tehsil were thoroughly mixed and made one composite sample of a Tehsil and associated seed mycoflora and their incidence were quantified through blotter and agar plate methods. A total 13 saprophytic as well as parasitic mycoflora belonging to nine (Alternaria, Aspergillus, Curvularia, Penicillium, Mucor, Rhizopus, Pyricularia, Fusarium and Helminthosporum) genera were detected through blotter and agar plate methods. Among mycoflora, maximum incidence of Fusarium sp. (2.42%), Aspergillus flavus (2.18%) and Curvularia lunata (1.96%) were recovered. Pyricularia spp. had maximum deteriorative and pathogenic impact in reducing seed germination (46%), in causing pre- (11.21%) and post emergence (8.88 %) mortality, in shortening radical (3.75 cm) and plumule length (5.25 cm) and in declining seedling vigour (414.00). In conclusion, huge loads of mycoflora adversely affect seed germination and plant health which ultimately results in poor stand of crop, yield and negative impact on consumer’s health.