Molecular markers may facilitate the identification of and selection for quantitative trait loci (QTL) that control economically important traits. The objective of the study was to compare the efficiency of selection among soybean [Glycine max (L.) Merrill] lines for seed yield based on single replication progeny-row-yield tests (PRYT), molecular marker loci selected by pedigree analysis, and a combination of PRYT and molecular marker data. A total of 380 random F3-derived lines from three populations were evaluated in the PRYT at Ames, IA, in 1997 and were genotyped for simple sequence repeats (SSRs) that had been chosen by pedigree analysis for their association with seed yield. The lines were divided into 13 tests for evaluation in 1998 at five or six Midwest locations in replicated yield tests. The average phenotypic correlation coefficient between the mean yield of lines in the 1998 test and their PRYT yield was 0.24, molecular marker score was 0.19, and index value was 0.35. The index was superior on the average to the PRYT or molecular marker score individually for selection of the highest yielding lines in the 1998 tests. The selection differential based on the index was superior on the average to the PRYT or molecular marker score individually in two of the three populations. Marker-QTL associations established by pedigree analysis should be useful alone or in combination with PRYT for selection among lines for seed yield in a cultivar development program.