A recurring issue in plant breeding is the narrowing of genetic diversity through continued selections by plant breeders to produce new cultivars. The objective of this thesis was to investigate the genetic and phenotypic diversity of two University of Guelph soybean breeding programs to characterize selections over decades of breeding. To study the genetic and phenotypic diversity of both University of Guelph soybean breeding programs, a panel of 296 pedigree-related genotypes from 1907 to 2016 was studied, the University of Guelph Germplasm Panel (UGGP). The genotypes were characterized using genotyping-by-sequencing (GBS) resulting in 40,307 single nucleotide polymorphisms (SNPs) and fragment sequencing resulting in 180 simple sequence repeat (SSR) markers. The markers were analyzed to determine differences between the two breeding programs and historical genotypes. The Guelph germplasm had overlap with historical genotypes, while the Ridgetown germplasm did not show the same pattern. Linkage disequilibrium (LD) decay was found with R2=0.2 at a distance of 600 kb genome-wide. Sliding window nucleotide diversity analysis found multiple genomic regions with differing patterns of low diversity between the groups of germplasm studied, which may attributable to breeder selection or crop domestication. One hundred and eighty Guelph and 96 Ridgetown genotypes were field-tested across multiple locations in 2015 and 2016 to identify trends in phenotypes over decades of soybean breeding. Some of the overall trends reported include: increasing oil concentration, increasing yield and decreasing linolenic acid concentration over year of release. In general, experimental germplasm had a wider range for the traits measured than other genotypes. Broad-sense heritability (H2) was high for many agronomic and seed traits in the UGGP genotypes. Analyzing the cost of SSR and SNP markers revealed SNPs markers being cheaper than SSRs to implement in a breeding program. Conversely, SSRs were used for marker-assisted selection (MAS) due to ease-of-use and short assay time. Overall, this thesis provides a baseline for the genetic and phenotypic diversity studies of soybean breeding programs, with the aim of assessing the genotypic and phenotypic changes in the germplasm. The findings in this thesis could be used by breeders to improve soybean breeding efforts.