Flowering time and branching type are important agronomic traits related to the adaptability and yield of soybean. Molecular bases for major flowering time or maturity loci, E1 to E4, have been identified. However, more flowering time genes in cultivars with different genetic backgrounds are needed to be mapped and cloned for a better understanding of flowering time regulation in soybean. In this study, we developed a population of Japanese cultivar(Toyomusume)×Chinese cultivar(Suinong 10) to map novel quantitative trait locus(QTL) for flowering time and branch number. A genetic linkage map of a F_2 population was constructed using 1 306 polymorphic single nucleotide polymorphism(SNP) markers using Illumina Soy SNP8 ki Select Bead Chip containing 7 189(SNPs). Two major QTLs at E1 and E9, and two minor QTLs at a novel locus, qFT2_1 and at E3 region were mapped. Using other sets of F_2 populations and their derived progenies, the existence of a novel QTL of qFT2_1 was verified. qBR6_1, the major QTL for branch number was mapped to the proximate to the E1 gene, inferring that E1 gene or neighboring genetic factor is significantly contributing to the branch number. Flowering time and branching types are important agronomic traits related to the adaptability and yield of soybean. Molecular bases for major flowering time or maturity loci, E1 to E4, have been identified. However, more flowering time genes in cultivars with different genetic backgrounds are needed to be mapped and cloned for a better understanding of flowering time regulation in soybean. In this study, we developed a population of Japanese cultivar (Toyomusume) × Chinese cultivar (Suinong 10) to map novel quantitative trait locus (QTL) for flowering time and A genetic linkage map of a F_2 population was constructed using 1 306 polymorphic single nucleotide polymorphism (SNP) markers using Illumina Soy SNP8 ki Select Bead Chip containing 7 189 (SNPs). Two major QTLs at E1 and E9, and two minor QTLs at a novel locus, qFT2_1 and at E3 region were mapped. Using other sets of F_2 populations and their derived progenies, the existence of a novel QTL of qFT2_1 was verified. QBR6_1, the major QTL for branch number was mapped to the proximate to the E1 gene, inferring that E1 gene or neighboring genetic factor is significantly contributing to the branch number.