Results/Conclusions In years with large infestations of insects, damage by chewing (Japanese beetle) and sucking insects (aphid) were greater in elevated than ambient carbon dioxide plots. The incidence of pathogen attack was greatest in warm, wet years, but, in contrast to insects, damage by viral, bacterial and fungal pathogens was reduced in elevated carbon dioxide plots. Transcriptional and biochemical analyses revealed that exposure to elevated carbon dioxide reduced the expression genes leading to the production of jasmonic acid (JA), a primary defense hormone, leaving soybean with reduced defenses against insects. A corresponding increase in salicylic acid (SA), a phytohormone that accumulates after pathogen attack, may have increased defenses against pathogens. These phytohormones often act antagonistically and are critical in mounting a proper defensive response to the array of challenges encountered in the field. Alterations in the relative production of JA and SA under elevated carbon dioxide may directly affect the trophic dynamics of plants in the field. By altering key aspects of primary and secondary metabolism, projected increases in atmospheric carbon dioxide will reset the co-evolutionary relationship between plants and organisms that attack them.