Round soybean seeds are sought-after for food-type soybean. Also the genetic control of seed geometry is of scientific interest. The objectives of this study were to estimate heritability and map quantitative trait loci (QTLs) responsible for seed shape traits. Three densely mapped recombinant inbred populations each with 192 segregants were used, Minsoy × Archer, Minsoy × Noir1, and Noir1 × Archer. A two rep two location experiment was conducted in Los Andes, Chile, and East Lansing, MI, USA. Seed height (SH), width (SW), length (SL), and seed volume (SV) as width × height × length were measured to determine seed shape. Heritability was estimated by variance component analysis. A total of 19 significant QTLs (LOD ≥ 3.7) in ten linkage groups (LG) were detected for all the traits. Only one QTL was stable across populations and environments and six were stable in at least two populations in both environments. The amount of phenotypic variation explained by a single QTL varied from 7.5% for SH, to 18.5% for SW and at least 30% of the genetic variation for the traits is controlled by four QTL or less. All traits were highly correlated with each other in all populations with values ranging from 0.5 to 0.9, except for SL and SW that were not significantly correlated or had a low correlation in all populations. Narrow sense heritabilities for all traits ranged from 0.42 to 0.88. We note that LG u9, u11, and u14 are hot points of the genome for QTLs for various traits. The number and genomic distribution of the QTLs confirms the complex genetic control of seed shape. Transgressive segregation was observed for all traits suggesting that careful selection of parents with similar phenotypes but different genotypes using molecular markers can result in desirable transgressive segregants.