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Peanut is an important food legume grown in semi- arid tropics of the world. Aspergillus fungus thrives in drought prevalent regions producing immunosuppressive carcinogenic aflatoxins in peanut seed. Identification and development of drought- tolerant genotype/s is the potential means to reduce aflatoxin contamination. We have determined differences in biochemical and molecular responses of peanut genotypes with varying degree of drought tolerance. Changes in protein and mRNA composition of seed in response to drought stress were measured using 2-dimensional electrophoresis and differential display RT PCR. Mass spectroscopy analysis revealed down-regulation of methionine rich proteins (MRPs) and arachin proteins in drought- susceptible (DS) genotypes, while these proteins continue to express in drought-tolerant (DT) genotypes. Up-regulation of mRNA transcripts in DT genotypes indicated their association with stress tolerance. Continued expression of these proteins seems to enhance drought tolerance, reduce aflatoxin level and enhance nutritional value of peanut.