Improvement of the quality and quantity of soybean seed constituents is one of the most important objectives in soybean breeding. Although the quality of seed constituents has been studied extensively, information on the quantity is still limited. In order to analyze the genetic basis of these traits, recombinant inbred lines (RILs) derived from a cross between Glycine max (L.) Merrill variety Misuzudaizu and variety Moshidou Gong 503 were planted in two environments and evaluated for seed protein and lipid contents. Protein and lipid contents were determined by NIR transmittance spectroscopy using an intact single seed. The broad sense heritability of the traits ranged from 0.73 to 0.79 in our RIL population. Single-factor analysis of variance, interval mapping and composite interval mapping were used to detect significant associations between the traits and genetic markers. A total of 17 QTLs, 10 for proteins and 7 for lipids, which were significant in at least one environment were identified. Each QTL explained the total phenotypic variation for protein and lipid contents in the range from 3.4 % to 29.7 % and 6.1 % to 10.1 %, respectively. Among all the detected QTLs, three for the protein content and three for the lipid content were detected in both environments. The negative correlation between protein and lipid contents was also confirmed. Epistatic interactions were detected in this study, as another source of genetic variation in our population. The results obtained in our study may serve as a base for analyzing the genetic control of protein and lipid contents and may eventually enable to change the seed constituents.