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Rice is the most aluminum (Al)-tolerant species among the small grain cereals, but there are great variations in the Al tolerance between subspecies, with higher tolerance in <i>japonica</i> subspecies than <i>indica</i> subspecies. Here, we performed a screening of Al tolerance using 65 <i>indica</i> cultivars and found that there was also a large genotypic difference in Al tolerance among <i>indica</i> subspecies. Further characterization of two cultivars contrasting in Al tolerance showed that the expression level of <i>ART1 (ALUMINUM RESISTANCE TRANSCRIPTION FACTOR 1)</i> encoding a C2H2-type Zn-finger transcription factor, was higher in an Al-tolerant <i>indica</i> cultivar, Jinguoyin, than in an Al-sensitive <i>indica</i> cultivar, Kasalath. Furthermore, a dose-response experiment showed that <i>ART1</i> expression was not induced by Al in both cultivars, but Jinguoyin always showed 5.9 to 11.4-fold higher expression compared with Kasalath, irrespectively of Al concentrations. Among genes regulated by ART1, 19 genes showed higher expression in Jinguoyin than in Kasalath. This is associated with less Al accumulation in the root tip cell wall in Jinguoyin. Sequence comparison of the 2-kb promoter region of <i>ART1</i> revealed the extensive sequence polymorphism between two cultivars. Whole transcriptome analysis with RNA-seq revealed that more genes were up- and downregulated by Al in Kasalath than in Jinguoyin. Taken together, our results suggest that there is a large genotypic variation in Al tolerance in <i>indica</i> rice and that the different expression level of <i>ART1</i> is responsible for the genotypic difference in the Al tolerance.