Soybean is one of the most important crop supplying protein and oil for food and industrial purpose worldwide. The genome sequence of cultivated soybean Williams 82 (Glycine max) has boosted genomic study of this ancient tetraploid Phaseoloid legume. Here we present an undomesticated soybean named W05 (Glycine soja) de novo genome using about 64.5-fold HiSeq2000 sequencing data. The assembly comprises 881.6 Mb of genome sequence with 61,388 protein-coding genes and about 358Mb (40.61%) repeat regions. As the direct progenitor of cultivated soybean, W05 represents higher gene diversity than Williams 82. In order to anchor scaffolds into linkages and detect trait-related genes across the whole genome, we used a RIL population by interspecific crossing between W05 and C08 (Glycine max) to construct high density genetic map. 96 RILs were genotyped via high-throughput whole genome re-sequencing strategy. 681.58 Mb (78.52% of assembly) sequences were successfully anchored into 20 chromosomes. Phenotype data of several quantitative traits were collected and corresponding QTLs were identified at the W05 genome sequence. The genome sequences of wild soybean and agronomic related QTLs provided by this study will promise a comprehensive understanding of this complex genome and accelerate soybean breeding programs.