Abstract Key message The production of adventitious roots partially counteracts the negative effects of waterlogging on the growth of Syzygium nervosum A. Cunn. ex DC. and Syzygium cumini (L.) Skeels. S . cumini was more responsive and suffered from larger negative effects than S . nervosum after the removal of adventitious roots. Context Adventitious roots contain gas channels and functionally replace or compensate for the loss of primary roots that usually decay during waterlogging. However, the importance of adventitious roots on growth in waterlogged woody plants varies with species. Therefore, there has been some controversy about whether adventitious roots have beneficial effects on the growth of waterlogged plants. Aims We assessed whether S . nervosum and S. cumini differentially responded to the ablation of adventitious roots during waterlogging and whether compensatory responses occurred in the primary roots in both species. Methods S . nervosum and S . cumini saplings were subjected to waterlogging and adventitious root removal for 120 days, and morphological, physiological, biochemical parameters, and biomass were recorded. Results All plants survived waterlogging, and produced adventitious roots at the shoot base. Waterlogging had negative effects on the growth of both species, but the effect was more severe in S . cumini than in S . nervosum as seen from the values of comprehensive evaluation and total biomass. However, S . nervosum compensated for the ablation of adventitious roots with increased primary root dry mass, primary root activity, total root length, root tip number, and peroxidase activity. Conclusions S . nervosum with a high proportion of adventitious roots would be at an advantage during waterlogging. The removal of adventitious roots was detrimental to the growth of both species, but S . nervosum exhibited less damage than S . cumini due to its compensatory physiological responses and its primary roots.