Seed borne fungi of 45 pea seed samples of Master-B cultivar were examined. These samples were collected from main production area of Egypt. A total number of 28 species, representing 19 genera of fungi was isolated and identified from pea seeds. The agar plate method was more accurate for detection of the most associated seed borne fungi compared with blotter method. Test tube agar method of 50 seeds from each of Master-B, Entsar 1, Entsar 2 and Sugar gum cultivars revealed incidence of 10 species, representing 8 fungi genera. These fungi were isolated from different seedling parts. Scanning electron microscopy (SEM) was used to examine seed borne fungi in dry seed surface of two pea cultivars Cambados (curly) and Oregon sugar (smooth).The curly cultivar hosted more fungi than the smooth one. Six categories of discoloration pea seeds were investigated using agar plate method. A total of 27 species, representing 19 genera were isolated and identified from pea seeds with different color categories. The effect of discoloration on seed characters and germination were examined. Discoloration of deteriorated seeds was associated with decreased total protein, total phenols, weight of 1000 dry seeds and seed germination percentages comparing with healthy ones. On the contrary, moisture contents in healthy seeds recorded lower percent compared with all discoloration seed categories and insect infection.