TaALMT1 and TaMATE1B promoter alleles are highly correlated with wheat growth in acidic soil with a high concentration of toxic aluminium. The aluminium (Al(3+)) resistance of 338 wheat genotypes with different geographic origins was correlated with morphological traits and TaALMT1 and TaMATE1B alleles. Both of these genes encode malate and citrate transporters associated with Al(3+) resistance mechanisms in wheat. Based on comparisons with the sensitive and resistant controls, the relative root growth was evaluated in hydroponic experiments and the plant performance was visually accessed in the field. The correlation between Al(3+) tolerance in the hydroponic and field tests was moderate (r = 0.56, P < 0.001). Higher selection pressure was observed in the field because a smaller number of genotypes was classified as resistant. The combination between the six TaALMT1 alleles and the two TaMATE1B promoters allowed the identification of 11 haplotypes that showed a high (r = 0.71, P < 0.001) correlation with Al(3+) resistance in the field, with the TaALMT1 alleles accounting for most of the correlation. The Brazilian wheat genotypes presented the best performance in soil, including eight cultivars with promoters usually associated with Al(3+) resistance and another six genotypes classified as moderately resistant but containing alleles usually associated with Al(3+) sensitivity. Although an increase in favourable alleles was observed over the past few decades, the average Al(3+) resistance in the field was not significantly different from that of older cultivars. The ease identification of the TaALMT1 and TaMATE1B alleles and their higher association with Al(3+) resistance along with the best genotypes identified here may be used for wheat-breeding programmes interested in increasing wheat Al(3+) resistance.