Because maize (Zea mays) is an annual species those working with it must frequently make crosses to preserve and periodically maintain populations. Random mating is performed either using hand-pollination techniques or in wind-pollinated isolated blocks. Eighty-two restriction fragment length polymorphism (RFLP) markers were used to examine samples of random mated, hand-pollinated BSSS(R) and BSCB1(R) maize populations to find out whether their genotypic proportions conformed to predicted outcomes of random mating. The majority of loci conformed to expectations for Hardy-Weinberg equilibrium (HWE). Excess homozygosity was observed at 87% of the loci where the null hypothesis of HWE was rejected. For pairs of polymorphic loci, linkage equilibrium was observed in the BSSS(R) and BSCB1(R) progenitor populations (fewer than 5% of all tests rejected the null hypothesis of equilibrium at the P≤0.05 significance level). The BSSS(R)CO, BSCB1(R)CO and BSCB1(R)C12 populations showed slight increases in the proportion of pairs of loci in linkage disequilibrium compared to the progenitors (approximately 8.4% of all pairs of loci rejected the null hypothesis at the P≤0.05 significance level). BSSS(R)C12 was an extreme outlier with 25.0% of all pairs of polymorphic loci displaying significant (P≤0.05) linkage disequilibrium. This result was likely caused by the artificial grouping of three BSSS(R)CO plants with 97 BSSS(R)C12 plants during sampling. Results from principal components analysis of all individuals based on RFLP alleles supported this interpretation. Overall, most of the observed deviations from equilibrium were likely to have been caused by positive assortative mating in the case of HWE, and natural selection for epistatic effects between unlinked loci in the case of linkage disequilibrium.