Plant breeders would like to predict which biparental populations will have the largest genetic variance. If the population genetic variance could be predicted using coefficient of parentage or genetic distance estimates based on molecular marker data, breeders could choose parents that produced segregating populations with a large genetic variance. Three biparental soybean Glycine max (L.) Merr. populations were developed by crossing parents that were closely related, based on pedigree relationships. Three additional biparental populations were developed by crossing parents that were assumed to be unrelated. The genetic variance of each population was estimated for yield, lodging, physiological maturity, and plant height. Coefficient of parentage was calculated for each pair of parents used to develop the segregating populations. Genetic distance was determined, based on the number of random amplified polymorphic markers (RAPD) that were polymorphic for each pair of parents. Genetic distance was not associated with the coefficient of parentage or the magnitude of the genetic variance. The genetic variance pooled across the three closely related populations was smaller than the genetic variance pooled across the three populations derived from crossing unrelated parents for all four traits that were evaluated.