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Microorganisms play an important role in affecting the seeds, of which fungi are the largest group. These pathogens are disastrous as they reduce the seed quality, germination and seedling vigor which reduces the optimum plant population in the field. Survey conducted in Konkan region revealed that the rice variety Ratnagiri-2 exhibited maximum seed discoloration (18%) while minimum seed discoloration (3%) was recorded in Ratnagiri-24, Karjat-4 and Sahyadri-3. In blotter test, association of seed borne fungi and the germination of different rice varieties revealed that, Karjat-4 and Panvel-3 recorded the association 20 per cent and 35.50 per cent respectively. In respects of germination, variety Karjat-4 recorded 98.50 per cent germination while the variety Panvel-3 recorded 60 per cent seed germination with maximum seed germination loss of 40 per cent. On Agar plate method, Ratnagiri-1 and Ratnagiri-73 showed maximum occurrence of seed-borne fungi (25%) and (27%) respectively. Nine fungal species viz., Fusarium moniliforme, Fusarium semitectum, Fusarium fusarioides, Curvularia lunata, Curvularia pallescens, Aspergillus niger, Trichoderma harzianum, Rhizopous stolonifer.