& Key message Hypoxia promoted distinct changes in the levels of hormones, amino acids and organic acids in the roots and shoots of a seedling from 2 Eucalyptus clones. These results indicate that modulation of hormone production, as well as specific chemical constituents associated with primary metabolism, contributes to the regulation of growth of Eucalyptus seedlings under hypoxic conditions. & Context Although floods in areas under Eucalyptus cultivation in Brazil negatively affect plant growth, chemical markers and/ or indicators of hypoxia contributes to the regulation.s & Aims This study aimed to evaluate the hormonal and metabolic alterations induced by hypoxia on seedling growth. & Methods Seedlings of Eucalyptus urograndis clones VCC 975 and 1004 were grown in liquid solution and submitted to bubbling with air or with nitrogen. Levels of indol-3-acetic acid (IAA), abscisic acid (ABA), ethylene, 1-aminocyclopropane-1-carboxylic acid (ACC), primary metabolite profile and photosynthetic parameters were evaluated after fourteen days. & Results Hypoxia did not affect shoot dry mass of the seedlings. However, it decreased stomatal conductance and photosynthetic CO 2 assimilation rate, and increased levels of ABA in the shoot. Hypoxia greatly reduced the dry mass and volume of roots, concomitantly with higher ACC and ethylene production. Moreover, hypoxia promoted distinct changes in IAA levels, and in amino acid and organic acid metabolism in roots and shoots. & Conclusion The biosynthesis of ABA, ethylene and IAA and its quantity in root tissues indicates the regulation of metabolism in response to hypoxia in Eucalyptus clones. Handling Editor: Erwin DreyerContribution of the co-authors: EFM designed, executed the study, and was the main contributor to the writing of the manuscript. Gustavo CV MAYRINK and Cleide R DIAS contributed to maintaining and completing the experiment. Camilo E VITAL performed the LC-MS analysis. Dimas M RIBEIRO, Ivo R SILVA, and Andrew MERCHANT assisted in the design of the experiment, analysis of the results and composition of the paper.Electronic supplementary material The online version of this article (https://doi.