Studies of the genetic structure of the Iowa Corn Borer Synthetic #1 (CB) and Iowa Stiff Stalk Synthetic (SS) maize populations are of particular significance because they serve as the model on which development of modern commercial hybrids are based. These populations are part of a reciprocal recurrent selection breeding strategy. With this strategy, plants from one population are crossed to plants from the opposite population (i.e. forming hybrids). These hybrids are tested, and the best ones are chosen. The plants crossed to form the chosen hybrids are identified and used to form the next generation in each population. The goal of each successive generation is to improve on the previous generation while maintaining variability within the populations. We measured the progress of this program by testing for between- and within-population level genetic differentiation by analyzing the variation at 86 SSR loci among plants sampled from eight groups (progenitors, Cycle 0, Cycle 1, Cycle 3, Cycle 6, Cycle 9, Cycle 12, and Cycle 15) in each population. The progenitors used to form these populations are highly polymorphic (3.8 alleles/locus and 0.56 expected heterozygosity). This polymorphism decreases through Cycle 15 (1.9 alleles/locus and 0.25 expected heterozygosity). Individual plants within groups have a larger amount of genetic variation (66%) than groups within each population (13%) or between populations (21%). Consistent with theoretical expectations is the repartitioning of variation from within populations (96% in progenitors) to between populations (58% in Cycle 15) over time. When testing for deviations from natural processes, we identified approximately 26 of the 86 SSR loci affected by a non-random process over time. These results implicate genetic drift with a more profound effect than artificial selection in small populations. Through the use of smaller sample sizes, we were able to analyze more intermediate groups than any previous work in these populations. These intermediate time points represent a comprehensive genetic look within CB and SS to evaluate the applied effectiveness of the reciprocal recurrent selection program in relationship to its theoretical framework.