Over-reliance on elite germplasm has led to a narrowing of the genetic diversity in North American soybean (Glycine max [L.] Merr) breeding lines and cultivars. Crosses between adapted elite cultivars and unadapted plant introductions may provide a means to alleviate the issue in developing new genetically more diverse, high yielding cultivars. In the past, favorable alleles for traits of interest have been found in exotic germplasm but the successful incorporation of such alleles into adapted cultivars has proved elusive and difficult. The objective of this study was to evaluate a population derived from the cross between an elite adapted cultivar and an elite exotic plant introduction to determine the genetic bases of adaptation to mega-environments in China vs. North America. A cross was performed between a Canadian cultivar, OAC Millennium and a Chinese elite cultivar, Heinong 38 to develop a recombinant inbreed line (RIL) population for QTL mapping. The RIL population was evaluated at 3 locations in China and 5 locations in Canada in 2004, 2005 and 2006. A linkage map was developed and yield QTL were identified by using single factor ANOVA and MapQTL5®. Among a total of 18 QTL, seven were universal across mega-environments, whereas 11 were mega-environment specific. Some but not all of these QTL have been reported previously as associated with yield increase in soybeans. Epistatic effects have been observed also for both the universal and mega-environment specific QTL. By understanding which type of QTL are present in either or both mega-environments, breeding strategies could be developed for better utilization of novel variation encompassed in exotic germplasm sources.