It has been known that SUB1A-1 confers submergence tolerance to rice (Oryza sativa L.). However, two indica rice genotypes, FR13A and Goda Heenati both carrying this gene, exhibited differential tolerance to submergence. Using oligonucleotide microarray combined with suppression subtractive hybridization, we identified a different number of submergence-responsive genes in each genotype. Two-way analysis of variance (ANOVA) of microarray data indicated that there was a high degree of congruency between transcriptional profiles of the two genotypes in response to submergence. Only two genes exhibited an opposing regulation pattern between genotypes after submergence and 324 genes were regulated by submergence only in one genotype and unchanged in their expression in the other, suggesting differential submergence responses. These genes were potentail candidates responsible for differential tolerance observed between genotypes. Gene ontology analysis demonstrated that they were significantly enriched in the processes involved in defense response and flavonoid biosynthesis. The current study provides novel clues for further understanding of the mechanism of submergence tolerance.