Background: Pulses are very crucial to meet the requirements of dietary proteins in the human diet especially for the predominantly vegetarian population in India. Pigeonpea [Cajanus cajan (L.) Millsp.] and chickpea (Cicer arietinum L.) are important pulses grown in India. The seeds of these crops are highly vulnerable to various microorganisms, both in the field and during storage, which play an important role in reducing the seed viability, germination and vigour causing considerable loss in yield and quality. There is no suitable recommendation available to maintain seed quality during storage of pulses, hence present study was undertaken. Methods: Seeds of pigeonpea and chickpea were treated with Captan and Carbendazim 50% WP fungicides @ 2.0 g/Kg of seed and stored under ambient condition. The samples were drawn at three months interval to assess the effect of storage on seed quality parameters. The vigour index I, seed germination and speed of germination of these seed samples were determined using ISTA rules. The detection of seed mycoflora in pigeonpea and chickpea seed samples was carried out by the blotter test as recommended by the International Seed Testing Association. Result: Total sixteen fungal species were recorded on stored seeds. Maximum incidence of Aspergillus fumigatus (19.83%), A. flavus (14.88%), A. niger (12.40%), Alternaria alternata (11.57%), Fusarium oxysporum (8.26%), Rhizopus stolonifer (7.44%) and Penicillium notatum (5.79%) were recorded on untreated seed of pigeonpea cv. P. 2001 after 18 months of storage. The per cent germination, speed of germination and vigour index of the stored seeds decreased with the increase in the storage period whereas the total number of fungi increased with the storage period, irrespective of treatments. Among the tested cultivars, germination in pigeonpea (cv. P. 991) remained above IMSCS ( greater than 75%) upto 18 months of storage under ambient storage condition. However, the germination of pigeonpea cv. P. 2001 seed could be maintained above IMSCS ( greater than 75%) up to 12 months only. In chickpea (local cultivar) seed, the germination remained above IMSCS ( greater than 85%) up to 9 months only under ambient storage, however seed treatment with either Captan or Carbendazim could prolong the longevity upto 12 months of storage.