Anthracnose, caused by Colletotrichum lupini is the disease that causes more damage in lupins around the world. Previously, we evaluated the relationship between alkaloid content and anthracnose tolerance in different varieties and breeding lines of L. albus. In the present work, an appropriate method to assess lupin isoflavones by Capillary Zone Electrophoresis (CZE) using borate alkaline buffer was developed. Genistin, licoisoflavone A, genistein and 2´-hydroxygenistein were detected in leaf, stem, bud and root of Lupins. We report amounts of these isoflavones in leaves of anthracnose tolerant and not tolerant L. albus and L. angustifolius at different development stages during the season 1998/99. Using two in-vitro bioassays against Colletotrichum lupini lupin isoflavones were tested. Our results show that licoisoflavone A, lupinalbin A, 2`-hydroxygenistein, licoisoflavone B, genistein and wighteone exerts from mild to strong fungitoxic activity. Indeed isoflavones, as natural protection, could play an important role in the resistance and tolerance of lupins against anthracnose