The transport of organic N compounds to the shoot in the xylem sap of nodulated soybean plants was investigated in an attempt to better understand the changes in N metabolism under root hypoxia (first 5 days of flooding), with different sources of N in the medium. NO3- is beneficial for tolerance of plants to waterlogging, whereas other N sources such as NH4+ and NH4NO3, are not. Nevertheless, in the presence of NH4+ high levels of amino acids were transported in the xylem, consistent with its assimilation. Some increase in the transport of amino acids was also seen with NO3- nutrition during waterlogging, but not with N-free medium. Ureide transport in the xylem was severely reduced during waterlogging, consistent with impaired N2 fixation under these conditions. The relative proportions of some amino acids in the xylem showed dramatic changes during treatment. Alanine increased tremendously under root hypoxia, especially with NH4+ as N source, where it reached near 70 % of the total amino acids present. Aspartic acid, on the other hand, dropped to very low levels and was inversely related to alanine levels, consistent with this amino acid being the immediate source of N for alanine synthesis. Glutamine levels also fell to a larger or lesser extent, depending on the N source present. The changes in asparagine, one of the prominent amino acids of the xylem sap, were most outstanding in the treatment with NO3-, where they showed a large increase, characteristic of plants switching from dependence on N2 fixation to NO3- assimilation. The data indicate that the lesser effectiveness of NH4+ during waterlogging, in contrast to NO3-, involves restricted amino acids metabolism, and may result from energy metabolism being directed towards NH4+ detoxification.