Seed dormancy is an important trait which determines the timing of seed germination. It is reported that seed dormancy is established during seed maturation, and broken during seed after-ripening. However, details of seed dormancy regulation mechanism are still unknown. Here, we focused on functions of a dormancy regulator gene, HYPNOS, in dormancy regulation. Mutants of HYPNOS seeds require longer dry storage time for dormancy release, showing its important role in dormancy regulation. We confirmed that GA signaling pathway is enhanced, and ABA signaling pathway is decreased in hyp-1 and hyp-2 seeds by quantitative real-time PCR results. Genetic relationships between HYPNOS and GA2ox2, a GA catalytic gene, or ABA2, an ABA biosynthetic gene were also determined. Besides plant hormones, several studies reported that DELAY OF GERMINATION 1 (DOG1) is a critical dormancy regulator. In this study, we also figured out that HYPNOS suppress DOG1 expression. Both of mRNA and protein levels of DOG1 were elevated in hyp mutant seeds compared to wild type. We confirmed that the increase of DOG1 levels was maintained throughout the seed after-ripening. In addition, DOG1 transcript and protein levels are higher in hyp mutant seeds during seed maturation. With these results, we suggested that HYPNOS might function to repress DOG1 mRNA and protein expression in seeds during seed after-ripening. We also confirmed that HYPNOS and DOG1 affects seed coat dormancy by comparing the germination frequencies of whole seed and coatless embryo in hyp mutant and DOG1 overexpressing seeds. Taken together, we suggested that HYPNOS negatively regulate seed dormancy through the alteration of DOG1 expression levels in Arabidopsis thaliana seeds.