Isoflavones are found in soybeans and have anti-microbial activity. In this study, 100 recombinant inbred lines were used to investigate the relationship between isoflavone levels in non-seed tissue and tolerance to 'Sclerotinia sclerotiorum' and 'Phytophthora sojae'. The distribution pattern of isoflavones varied in different tissues. High levels of genistein in stems of control plants was associated with low necrosis scores to ' S. sclerotiorum'. High levels of total isoflavones in roots of plants inoculated with 'P. sojae' was associated with high tolerance scores. Satt308 and Satt316 were associated with tolerance to 'S. sclerotiorum ', explaining 6.0% of the variance in the population. Satt288, Satt330 and Satt472 were associated with tolerance to 'P. sojae ', explaining 6.7%, 5.2% and 33.9% of the variance in the population. Four of these markers were also associated with the isoflavone levels in corresponding tissues providing a genetic link between isoflavone levels and tolerance to these pathogens.