Soybean (Glycine max [L]. Merr.) is one of the most economically important leguminous seed crops that provide the majority of plant proteins, and more than a quarter of the worlds food and animal feed. It is suggested that soybean was domesticated from its annual wild relative, G. soja Sieb Zucc, in China approximately 5,000 years ago, resulting in a multitude of soybean landraces that were adapted to various climate environments. The research on soybean in China lags behind other major crops, in addition approximate 60% of soybean consumed in China is imported from other countries. A better understanding of soybean genetics and genomics will advance breeding varieties with improved yield, quality, and stress tolerance. We will combine association mapping, QTL mapping, map-based cloning along with comparative genomic approach, as well as construction and utilization of mutant database to identify genes controlling important agronomical traits and to apply them into the soybean breeding, which will facilitate soybean germplasm enhancement and benefit soybean production.