New drought-tolerant line IR74371-70-1-1 released as “Sahabhagi Dhan” in India was infected with brown spots during dry season 2010. Symptoms on 15 days old seedlings included stunted and yellow growth, with brown spots on leaves. The associated microflora was isolated and identified by molecular techniques. Taxonomy report by BLAST of NCBI indicated that the pathogen isolated during this investigation, belonged to Ascomycota, Dothideomycetes, Pleosporaceae. It had 99% similarity with Bipolaris oryzae, and 97% similarity with Cochliobolus sativus. Appropriate control / management practices for cultivation of this new drought tolerant rice variety must be adapted to avoid crop losses due to this devastating disease.