Abstract: Good quality seed is the prerequisite to agriculture and though of such vital significance very less attention has been paid to their efficient storage and storage losses. The present study was undertaken to screen for isolation and percent incidence of seed borne mycoflora wherein two Mungbean varieties viz. HUM-4 and HUM-12 were screened by standard blotter paper and agar plate methods at the different period of storage. Seeds of Mungbean varieties were obtained from agriculture farm, Banaras Hindu University, Varanasi. The surface sterilization was done by 0.1% mercuric chloride (HgCl2) for 1 min and washed thoroughly with distilled water. Both sterilized and unsterilized seeds were used for detection of seed borne pathogen. A total of 22 different fungi including one bacterial isolate belonging to 12 distinct genera were isolated were from these seed samples. The percentage incidence of different fungi varied with the storage periods. Aspergillus niger recorded at maximum level in 22.33, 43.27, 49.95, 19.98, 22.98 and 39.00% in Agar plate method from fresh, 180 and 360 days period of storage in HUM-4 as well as HUM-12 genotype. Highest incidence of seed borne fungi was recorded in genotype HUM-4 in Agar plate followed by HUM-12 through blotter condition. In all storage period unsterilized seed yielded most number of seed borne fungi as compared to sterilized seed. Result revealed that in all storage period Aspergillus sp. Penicillium sp. Curvularia lunata were recorded highest in HUM-4 through Agar plate method, Fusarium sp. were recorded highest in HUM-4 blotter method and lowest in HUM-12 agar plate methods, Rhizopus Cephaliofhora irregularis, Chaetomium globosum and Cladosporium cladosporoids in HUM-12 under Agar condition. Result showed that maximum number of fungi belonged to Deuteromycotina (68. 98%) followed by Ascomycotina (13. 89%) and Zygomycotina (9. 09%).