One of the limiting factors in the growth and development of plants is soil acidity due to high aluminium (Al) content. The aim of this research was to determine the micronutrient contents, photosynthetic pigments, gas exchange and morphological parameters, and to explain the possible tolerance mechanisms involved in two species of the genus Eucalyptus that were exposed to low and high aluminium concentrations. The experiment was conducted in a factorial completely randomised design, with two aluminium concentrations, viz., 0.08 (low) and 1.60 (high) mM Al, and two species, i.e., Eucalyptus platyphylla and Eucalyptus grandis. High Al concentration increased the Al contents in E. platyphylla and E. grandis by 104 and 29%, respectively. Significant reductions of Fe, Zn and Mn contents were detected only in E. platyphylla. Reductions on chlorophyll b and total chlorophyll were observed in both the species, which were more intense in the E. platyphylla. Net photosynthetic rate and water use efficiency increased under high Al concentration, whereas stomatal conductance and transpiration rate decreased in E. grandis. Growth characteristics decreased under high Al concentration in E. platyphylla and increased in E. grandis, while opposite response was observed in both species under low Al concentration. Our results described clearly that E. platyphylla is sensitive, while E. grandis is tolerant to Al. The tolerance mechanism of E. grandis can be explained by the maintenance of the iron, zinc and manganese supplies, combined with an increase in the chlorophyll a, net photosynthetic rate and water use efficiency, resulting in the mitigation of the Al effects on growth parameters.