Grain discolouration, a complex disease of rice is a new enemy to rice crops around the world, and it is becoming increasingly important due to the qualitative as well as quantitative loss of harvested crop. The present study was carried out on the ten different variety of rice (MEX-73, NLR-33892(Parthiva), MEX-48, MEX-61, PR-126, PR-128, PR-129, PR-130, Pusa-basmati -7 and Pusa basmati-1121). The incidence was calculated in one metre square quadrants randomly marked in the plot, where the highest incidence was observed in PR-126(36.23%) and the least was Pusa basmati-1121(19.77%). Several seed borne fungi were detected using blotter paper method. The Mycoflora observed were Curvularia sp., Fusarium sp., Bipolaris oryzae, Sarocladium sp., Aspergillus sp, Penicillium sp. The maximum frequency was observed for Aspergillus (25.73%) followed by Penicillum (24.53%), and the least observed was Bipolaris oryze(1.73%). The identity of the Aspergillus was confirmed using Inter transcribed Spacer primers (ITS1 & ITS4).