The maize (Zea mays L.) populations Iowa Stiff Stalk Synthetic (BSSS) and Iowa Corn Borer Synthetic No. 1 (BSCB1) have undergone reciprocal recurrent selection (RRS) since their establishment in 1949. This study focused on molecular genetic variation of the progenitor inbred lines used to synthesize BSSS and BSCB1 as well as elite inbred lines derived from different cycles of selection. Our objectives were to investigate changes in allele frequencies and genetic diversity from progenitors to derived lines and evaluate trends in genetic diversity among elite lines derived from early and advanced selection cycles. Genotypic data for 105 restriction fragment length polymorphism (RFLP) loci were collected from four groups: 16 progenitors and 18 elite lines derived from BSSS, 12 progenitors and 7 elite lines derived from BSCB1. Each progenitor group had a broad genetic base but both were genetically similar. The groups of derived lines diverged substantially from each other. A larger Roger's distance was found between the groups of lines derived from advanced cycles than between the groups of lines derived from Cycle 0. Allelic variation within each group of lines, however, decreased just slightly with the elite lines capturing almost 75 and 67% of the allelic variation present in the progenitor lines of BSSS and BSCB1, respectively. The results of this study confirm the long-term potential of this RRS program and the importance of the choice of broadly based progenitor materials.