Green plants (Viridiplantae) include half a million diverse species and have evolved to survive in almost every environment on Earth. Considering that a large variety of both genetic and phenotypic diversity has been observed across the plant kingdom, a long-standing question still remains: How has the diversity in plant form and function emerged from changes in its genome? Everything we currently know about the genes that govern developmental morphology in plants comes from a small proportion of model and crop species. However, ongoing efforts to assemble more plant species and the coupling of phylogenetic and genomic studies could soon reveal the genetic signatures of past evolutionary change and the molecular basis driving the diversification of future species. Using comparative genomics of closely related species, I aim to investigate the molecular basis of root development in the economically significant plant, Glycine max (soybean), and related species within Leguminosae. I established a comparative genomics pipeline for soybean relatives in distinct legume clades and characterized differences in root anatomy and morphology across different legume species. With these tools, I utilize a multidisciplinary approach involving genomics, phylogenetics, and developmental biology to determine the genes and gene networks that have previously evaded detection. This work will advance current comparative genomics methods by focusing on establishing the evolutionary relationship that drives variation in root morphology in legumes.