The acquisition of inorganic matter from soil is fundamental to the survival of all plant life on earth, and is of particular concern regarding agriculturally relevant species. The summation of the inorganic constituency of an organism is collectively known as the ionome. The study of the ionome, which is called ionomics, has the potential to impact major agricultural concerns facing the planet such as nutrient use efficiency, heavy metal toxicity, soil salinification, bio-fortificiation, and exclusion of toxic metals or metalloids from the human diet. Partly due to the challenge of phenotyping such a complex network of correlated phenotypes amid tremendous environmental variation, the genetic architecture of the rice ionome is poorly characterized. This dissertation explores the genetic underpinnings of the phenotypic variation of the rice ionome and demonstrates the tractability of using controlled environments to survey large crosssections of genetic variation. Genetic analysis was performed using both linkage and association mapping on a diverse and well-characterized bi-parental recombinant inbred line mapping population and panel of 400 diverse Oryza sativa accessions collected from around the world, respectively. The analysis identified 362 significant regions of the rice genome controlling the accumulation of 24 mineral elements in rice roots and shoots under hydroponic growth conditions. Seventy nine of these significant regions co-localize with known and putative candidate genes. Haplotypes at candidate genes for shoot molybdenum and shoot sodium concentration along with physiological and gene expression experimentation validates the hypothesis that these candidates are likely to be responsible for a large portion of the phenotypic variance present in our populations. Furthermore we demonstrate that the aus sub-population excludes significantly more sodium from the shoot tissue and accumulates significantly more molybdenum than any other sub-population, and especially indica. Admixture analysis identified that aus haplotypes at candidate genes identified by the genetic mapping results significantly increase molybdenum shoot concentration and decrease sodium shoot concentration when present in otherwise indica-like genomes. The results from this study form the basis for extensive follow-up research not only on the candidates identified for sodium and molybdenum but also for the 22 other elements in both above and below ground tissues.