Plant height is an important agronomic trait that affects grain yield. Previously, we reported a novel semi-dominant dwarf mutant, D-h, derived from chemical mutagenesis using N-methyl-N-nitrosourea(MNU) on a japonica rice cultivar, Hwacheongbyeo. In this study, we cloned the gene responsible for the dwarf mutant using the map-based approach. Fine mapping revealed that the mutant gene was located on the short arm of chromosome 1 in a 48 kb region. Sequencing of the candidate genes and rapid amplification of cDNA ends-polymerase chain reaction(RACE-PCR) analyses identified the gene, d-h, which encodes a protein of unknown function, but whose sequence is conserved in other cereal crops. Real-time (RT)-PCR analysis and promoter activity assay showed that the d-h gene was primarily expressed in the nodes and the panicle. In the D-h mutant plant, the gene was found to carry a 63-bp deletion in the ORF region, which was confirmed to be directly responsible for the mutant’s gain of a functional phenotype by subsequent transgenic experiments. Since the mutant plants exhibit a defect in the GA response, but not in the GA synthetic pathway, it appears that the d-h gene may be involved in a GA signaling pathway.