Methionine is one of three essential amino acids that are nutritionally limiting in maize, which is a major component of animal diets. Diets consisting mainly of maize must be supplemented with other sources of methionine to provide adequate nutrition. Plant breeding strategies have been implemented to increase the level of methionine in maize. The objective of this study was to genetically characterize two programs involving recurrent selection for grain methionine content. These programs started with the synthetic populations BS11 or BS31. We sought to determine the genetic effects this selection process has had on the genome. Single nucleotide polymorphism (SNP) markers distributed across the genome and in gene regions potentially related to methionine levels were examined using allele frequency based and linkage disequilibrium (LD) analyses. The percentage of polymorphic loci decreased through the cycles of selection in both populations and alleles present in the starting populations were lost. The two measures of LD used in this study, D' and r2, demonstrate an increase in disequilibrium across the genome for both BS11- and BS31- derived populations suggesting selection occurred at multiple loci. Several genetic loci exhibited allele frequency changes that paralleled the advancement of the selection program.