There continues to be improvements in seed yields of soybean [Glycine max (L.) Merr.] by conventional breeding, but molecular techniques may provide faster genetic gains. The objective of this study was to identify quantitative trait loci (QTL) associated with the agronomic traits seed yield, lodging, plant height, seed filling period, and plant maturity in soybean. To achieve this objective, 101 F6-derived recombinant inbred lines (RIL) from a population developed from a cross of N87-984-16 x TN93-99 were used. Experiments were conducted in six environments during 2002 and 2003. Heritability estimates on an entry mean basis from data combined across environments ranged from 0.12 to 0.65 for seed yield and seed filling period respectively. Composite interval mapping detected one QTL for yield (near Satt076), two for lodging (near Satt225 and Satt593), and four for maturity (near Satt263, Satt292, Satt293 and Satt591) in this population. Additional environmentally sensitive QTL for these traits, and for seed filling period and plant height are also reported. The QTL associated with agronomic traits that we report and the recently released germplasm (PI 636460) from this population may be useful in soybean breeding programs.