The objective of this thesis was to investigate the genomic changes that have occurred due to the effects of long-term artificial selection applied by soybean breeders. A total of 42 cultivars from six different breeding programs, comprising the multi-generational pedigree of OAC Bayfield were genotyped with molecular markers and chromosomal inheritance was tracked throughout the pedigree. The graphical genotype profile of the 20 chromosomes revealed substantial allelic structure that has been built up in certain chromosomes, in the form of specific linkage blocks, which have been conservatively inherited. A selective sweep analysis using microsatellite markers was performed using the members of OAC Bayfield’s pedigree to identify genomic regions that have retained a molecular selective signature through OAC Bayfield in the varieties derived from it. Overall, there was a high level of agreement between the identified quantitative trait loci (QTL) and the phenotypic traits that would have been expected to be under breeders’ selection.