Soybean (Glycine max (L.) Merr.) is the second most widely planted crop in the United States by acreage, but yet its genetic resources, mapping methodologies, and breeding improvements lag behind those of other major crop species. In the 20th century, soybean researchers gathered a wealth of natural soybean genetic diversity in the forms of soybean’s wild relative G. soja, soybean landraces, soybean elite lines, and spontaneous mutants. Starting in that same century, researchers began inducing soybean mutations through chemical or irradiation mutagenesis to generate new phenotypes. In the 21st century, these mutagenesis efforts have expanded and have been coupled with new genomics tools to enhance soybean functional genomics. These new mutagenesis efforts and genomics tools will be discussed in chapter one. One of the challenges facing soybean is the difficulties in gene mapping, cloning, and validation. A major focus of this dissertation is the adaptation of new genomics tools and mapping methodologies to soybean in order to facilitate the identification of causative mutants in soybean. Chapter two demonstrates a more classical approach to gene mapping and soybean whole plant transformation to identify the causative loci for three spontaneous chlorophyll deficient mutants. In contrast, chapter three utilizes a combination of new genomics approaches to map and clone a fast neutron induced mutant and validates the result using both a second mutant allele from a historic soybean mutant and transformation of an Arabidopsis mutant. Chapter four builds off of the results of chapter three in leveraging the genomic mapping approach to clone a spontaneous canopy architecture mutant. Several unexpected results and conclusions are reported in the following chapters. Chapter two provides evidence to challenge the widely held idea of gene redundancy in soybean provides an effective buffer against mutations. Additionally, to our knowledge, the research of chapter two reports the first instance of identical mutations affecting two different paralogs resulting in nearly identical phenotypes. Chapter three demonstrates that array comparative genomic hybridization technology and whole genome sequencing of mutant and wild-type bulks can be effectively combined to map and clone a fast neutron mutant from a small F2 population. The chapter also provides an example of the high complexity of mutations that can result from fast neutron irradiation. Chapter four describes the mapping and characterizing a short petiole mutant. The research identifies that the short petiole trait (lps1) is due to a three base-pair in frame insertion in an uncharacterized gene. It was found that the mutation decreases petiole length primarily by decreased cell length and that the short petiole trait could be agronomically beneficial through improved harvest index. The results from chapter four suggest that there is the capacity to improve soybean’s productivity and agronomics through modifications to canopy architecture, as has been demonstrated in other major crop species. The fifth and final chapter discusses potential future directions for soybean genomics research. New population designs with improved efficiency are described. Additionally, suggestions are made for how to utilize current technologies to improve next generation population designs.