Pigeon pea (Cajanus cajan L.) seeds mycoflora was studied and subsequently determine their effect on seed germination and seedling growth in pot condition. Seed sample were examined in agar plate and blotter method showed association of nine fungi belonging six genera i.e., Aspergillus niger, Aspergillus flavus, Fusarium oxysporum, Fusarium moniliforme, Fusarium udum and Alternaria alternata. Seed mycoflora and their culture filtrate caused considered reduction in germination per cent and seedling growth as compared to untreated check. Lowest seed germination recorded by Aspergillus niger in both culture filtrate (43.00%) and seed inoculated (56.00%).The effect of different chemical fungicides, bio-agents and phyto-extracts on seed mycoflora, germination and vigour index of pigeonpea was evaluated. The seed treatments improved seed germination, vigour index and reducing seed borne mycoflora of pigeonpea seeds. Different fungicides, bio-agents and phyto-extracts were evaluated as seed treatment. In fungicides, Matalaxyl 8% + Mancozeb 64% @ 0.2% was found superior in seed germination (93.33%), shoot length (11.23cm), root length (13.67cm) and vigour index (2323.73) whereas, in bio-agents Trichoderma viride was found most effective in seed germination (88.00%), shoot length (9.03cm), root length (11.17cm) and vigour index (1777.46). seed treatment with phyto-extracts Neem seed extract gave more seed germination (78.67%), shoot length (7.97cm), root length (9.20cm) and vigour index (1350.00) compared to control.