Molecular markers provide a rapid approach to breeding for desired agronomic traits. To use them, it is necessary to determine the linkage between quantitative trait loci (QTLs) and such markers. The objective of this research was to determine such linkage in recombinant inbred (RI) soybean [Glycine max (L.) Merrill] populations. To do this, RI soybean segregants were characterized for molecular genetic markers and traits measured in several different environments. QTLs then were identified by interval mapping. Agronomic traits were measured and compared in large (about 240 segregants) RI populations derived from crosses between the cultivars Minsoy and Noir 1 (MN population), Minsoy and Archer (MA population), and Noir 1 and Archer (NA population). The MA and NA populations were grown together as two replications in each of four environments. Measurements from the MN population were reported previously and were taken from three replications grown in four environments. Traits measured were plant height, lodging, date of flowering, reproductive period, maturity, yield, seed weight, seed oil, seed protein, leaf length, and leaf width. Additional traits were derived from these primary measurements. Each of the three RI populations was also characterized by a large (>400) number of molecular genetic markers including RFLP (restriction fragment length polymorphism) and SSR (simple sequence repeat polymorphisms). QTLs were identified for all of the primary and derived traits at a significance level ≥LOD 3 on 17 of the 20 linkage groups and tended to be clustered on three. QTLs with major effects (R2 > 10%) were identified for all traits, and for many, these explained more than half of the heritable variation. Comparison of QTLs between the three RI populations established that for the majority of the traits, only two alleles could be identified. In only a few instances could a third allele be detected. Many of the significant QTLs identified in one population were confirmed in another. However, an almost equal number were found in only one population, suggesting that a dependence on the genetic background for expression (epistasis) was common.