Dominant early heading (DEH) in rice (Oryza sativa L.) is of interest in both breeding and genetics. The genetic mechanisms underlying DEH have remained largely unclear. We have developed a near-isogenic DEH line without yield drag named DEH 229 by sister-line back-cross (BC) breeding with MH63, a restorer, as the genetic background. We conducted a pilot genetic investigation under both short-day (SD) and long-day (LD) conditions. The DEH line harbored only 1.06％variation in the genome sequence relative to MH63. The variants were distributed throughout the genome. Using QTL mapping by sequencing (QTL-seq) on an F2 population derived from a cross of MH63 × DEH 229, 57 loci were detected under the SD condition. Joint mapping employing a genome-wide association study with accessions from the 3000 rice genome sequencing project (3K-RG), reduced the number of QTL by 43.9％. Using Rice Functional Genomics & Breeding (RFGB) database, the number of SNP cluster regions within the QTL regions reduced by 27.3％. Further comparison of the gen-ome variation between DEH 229 and MH63 in addition to gene annotation information revealed a new DEH allele of DTH3 with multiple variable sites as a possible major factor underlying the early-heading phenotype of DEH 229. An InDel marker, ZMEH 1, was designed based on the variation between DEH 229 and MH63 within this region. It accounted for 86.0％of heading date variation under both SD and LD conditions in 109 ran-domly chosen progeny derived from extreme lines of the MH63 × DEH 229 population. This study reveals the genetic complexity of DEH in the near-isogenic line and may provide use-ful material and marker information for plant molecular breeding.