To determine the impact of 3 cycles of selfing and selection on inbreds of maize in field performance and molecular variation, seeds of 6 A- lines, 6 maintainers (B- lines) and 6 restorers (R- lines) were planted. That was on the farm of Field Crop Sci., Coll. of Agric., Univ. of Baghdad across 6 planting seasons during 2008-2010. Previous published results of this article showed that performance of selected inbreds was different as compared to original populations. Then, samples were taken from these inbreds and analyzed for their DNA. Ten RAPD primers were used and gave 139 DNA bands of molecular weight ranged between 264-2717 bp. Coefficient of Nei and Li of genetic similarity (GS) revealed that similarity ranged between 76% to 97% between original and selected populations. The highest GS (97%) was between inbreds R6-o and R6-s, while the lowest GS (76%) was between inbreds R2-o and R2-s. However, genetic similarity among all inbreds ranged between 57% to 89%. Meanwhile inbreds of higher genetic diversity did not give higher performance or higher hybrid vigor. This implies that hybrid vigor is not necessarily correlated with genetic diversity, or such tests need more primers, or hybrid vigor is correlated with a specific favorable number of diversed QTL integrate so well when their inbreds crossed.