Aluminium ion (Al3+) toxicity and hydrogen ion (H+) activity are the major constraints for plant growth in acid soil. This study was undertaken to determine the effect of pH and Al on the growth response and changes in root morphology of Al-tolerant (ET8) and Al-sensitive (ES8) wheat seedlings. Different levels of AlCl3 and CaCO3 were added to the soils to manipulate soil pH and extractable Al. The results showed that the bulk soil pH remained constant at pH 4.1 with further applications of AlCl3, and that the seedlings died at the 200 mg AlCl3/kg treatments. The ET8 seedlings responded better than the ES8 seedlings in both low and high Al and pH. The ET8 seedlings had higher root surface areas and root tip numbers than the ES8 seedlings in the Al treatment. In contrast, the ES8 had higher root diameters than the ET8 seedlings due to the elevated Al supply. Apoplast Al increased with the increase of soil available extractable Al, and declined with the decrease of soil extractable Al. The ET8 seedlings accumulated more Al in their apoplast than the ES8 seedlings. This study concluded that accumulation of Al in the apoplast is also involved in Al tolerance mechanism with the addition of organic acid exudation.