Seed yield mega-environment-universal and specific QTL (QTL(U) and QTL(SP), respectively) linked to Satt100, Satt130, Satt162, Satt194, Satt259 Satt277 and Sat_126, have been identified in a population derived from a cross between a Chinese and a Canadian soybean [Glycine max (L.) Merrill] elite line. The variation observed in yield could be the consequence of the variation of agronomic traits. Yield-component traits have been reported in the literature, but a better understanding of their impact at the molecular level is still lacking. Therefore, the objectives of this study were to identify traits correlated with yield and to determine if the yield QTL(U) and QTL(SP) were co-localized with QTL(U) and QTL(SP) associated with an agronomic trait. A recombinant inbred line (RIL) population was developed from a cross between a high-yielding adapted Canadian and a high-yielding exotic Chinese soybean elite line. The RIL were evaluated in multiple environments in China and Canada during the period from 2004 to 2006. Four yield QTL(U,) tagged by markers Satt100, Satt277, Satt162 and Sat_126, were co-localized with a QTL associated with an agronomic trait, behaving as either QTL(U) or QTL(SP) for the agronomic trait. For example, the yield QTL(U,) tagged by marker Satt100 was associated also with 100 seed weight, pods per plant, pods per node, plant height, R1, R5, R8, oil content and protein content in all Canadian environments, but only with pods per plant, pods per node, plant height, R1, R5, R8 and oil content in two or more Chinese environments. No agronomic traits QTL were co-localized with the yield QTL(U) tagged by the marker Satt139 or the yield QTL(SP) tagged by Satt259, suggesting a physiological basis of the yield in these QTL. The results suggest that a successful introgression of crop productivity alleles from plant introductions into an adapted germplasm could be facilitated by the use of both the QTL(U) and QTL(SP) because each type of QTL contributed either directly or indirectly through yield-component traits to seed yield of RILs.