Aims: Poor soil aeration can be the result of poor soil drainage, soil compaction, or flooding of the root zone, and tolerance to root hypoxia is determined by rootstock characteristics. Based on this assumption, we aimed to verify whether cherry rootstocks can be classified according to their tolerance to poorly aerated soils based on their root growth traits. Methods: Six cherry rootstocks, ‘Mazzard F12/1’, ‘Gisela 6’, ‘Colt’, ‘Maxma 14’, ‘Maxma 60’ and ‘Cab 6P’, were established in 300L containers under field conditions and they were evaluated. Three soils with different textures were selected to generate different air-filled porosities by controlling the volumetric water content: 21% (Ɛα21%), 16% (Ɛα16%) and 9% (Ɛα9%). Vegetative growth, photosynthetic parameters and fine root growth were measured during the 2013-2014 season. Results: In soils with a low air content, Ɛα9%, ‘Colt’ and ‘Maxma 60’ rootstocks increased total fine root production by increasing root growth rates in the last phase. ‘Colt’ and ‘Maxma 60’ can be classified as tolerant rootstocks. In contrast, ‘Mazzard F12/1’ and ‘Gisela 6’ reduced shoot growth by 51.5% and 42.4% and reduced the maximum rate of photosynthesis (Amax) by 69% and 78%, respectively, compared with contrasting soil aeration, resulting in a reduction in total fine root output in poorly aerated soil. They were classified as sensitive rootstocks. Conclusions: Higher fine root production and lower root mortality were the major root traits of tolerance that improved photosynthetic performance and were associated with high photosynthetic capacity under a prolonged low oxygen content in the soil.