Rice seed dormancy is an important trait related to the preharvest sprouting resistance of rice and is controlled by a polygene network. To identify the genes involved in this process, transcriptome analysis was applied to strong seed dormancy indica cultivar N22 and its weak dormancy mutant Q4646. The results showed that 280 genes were significantly upregulated and 244 genes significantly downregulated in the seed of Q4646 as compared to N22 during 25 to 28 days after heading. These genes were mainly involved in stress response, C-compound metabolism, plant development, DNA processing, and lipid metabolism. Some of these genes were colocalized with several reported dormancy QTLs, suggesting that they are possibly candidate genes underlying rice seed dormancy. Our work provides important clues for future effort to clone seed dormant genes in rice.