We examined the ability of seagrasses to take up dissolved organic nitrogen (DON) with leaves (in situ) and roots (laboratory) in an oligotrophic tropical offshore meadow in Indonesia using 15N‐labeled nitrogen (N) substrates. We compared the uptake of urea and amino acids with that of ammonium (NH4+) and nitrate (NO3−) and determined uptake kinetics of amino acids for the seagrasses Thalassia hemprichii, Halodule uninervis, and Cymodocea rotundata in comparison with the macroalgae Sargassum sp. and Padina sp. Uptake rates of small DON substrates for macroalgae were higher than those for seagrass leaves for all N substrates, but the seagrass roots also had a considerable uptake capacity. Seagrass leaves preferred urea, NH4+, and NO3− over amino acids, and there were differences between species. Seagrass roots, however, took up amino acids at rates comparable to NH4+, whereas uptake rates of urea and NO3− were much lower. The ability to take up DON enables seagrasses and macroalgae to shortcut N cycling and gives them access to additional N resources. In oligotrophic environments, uptake of amino acids by roots may provide seagrasses with a competitive advantage over macroalgae.