The storage fungi damage the grains in several ways; they reduce the germination capacity, produce undesirable odor and kernel discoloration, decrease the food value, and also produce toxins that are injurious to the health of consumers. Therefore, this study was designed to investigate the presence, and determine the identity, and incidences of major fungal pathogens associated with crop seeds. Totally fifty-eight seed samples of nine crops were used to investigate the presence and incidence of fungi associated with them in Potato Dextrose Agar (PDA) media. Results of the study revealed that a total of 9 fungi belonging to 8 genera viz. Penicillium sp., Aspergillus flavus, Aspergillus niger, Bipolaris sp., Botrytis sp., Alternaria sp., Ascochyta sp., Fusarium oxysporum, and Rhizopus sp. were isolated from samples. The infection percentage varied from 0-100% in samples of seed multiplication store. Most varieties of crops showed 100% infection followed by 97.5% (HB1307 of barley and Alidoro of wheat), 95% (Kingbird of wheat and RIB13/14 of nug), 90% (Kuncho of teff), 50% (Holetta-1 11/12 of gomenzer), 20% (Ginchi-1 11/12 of nug and Yellow Dodola15/16 of gomenzer), 10% (Shambu 17/18 of oat), and 5% (Shambu 11/12 of oat, S-67 17/18 of gomenzer and Fogera 10/11 of nug) except linseed samples 0%. In general, seed-borne fungi were present in most seed samples of cereals, oils, and legume crops. Some of the identified fungi are potential producers of mycotoxins, thus their presence is important in terms of reduced food safety for humans and animals. In addition, some seed-borne fungi were also the causal agents of diseases of the roots, stems, and leaves of crops. Fungal incidence of seed was highly associated with storage conditions of the independent variables, such as temperature and relative humidity of storage. So, it is suggested that the management of fungal growth, mycotoxin production, and fungal contamination incidence of seed should be investigated and confirmed with additional studies.