Exposure to toxic elements through contaminated food poses significant health risks to consumers globally. Metal toxicity, particularly cadmium (Cd), has been identified as a major health concern. Regulatory bodies like the European Food Safety Authority (EFSA) and the World Health Organization (WHO) have recognized cacao beans and chocolate as sources of Cd in the human diet, prompting the establishment of safe upper limits for Cd in these products. Additionally, California’s Proposition 65 addresses dietary exposure to Cd by establishing safe harbor levels for toxic elements, highlighting the importance of monitoring and regulating Cd levels in food. The literature reviewed on this topic is included in Chapter 1. This thesis examines molecular mechanisms and physiology of cadmium (Cd) uptake in cacao, focusing on the Heavy Metal ATPase (HMA) gene family known for its role in Cd transport. The research provides insights that could aid development of future mitigation practices and selection of low Cd-accumulating genotypes. Chapter II describes the identification and evolutionary analysis of the HMA gene family in Theobroma cacao L. Eight genes were identified that encode for HMA proteins, including 2 IB-2, Zn²⁺, and Cd²⁺ transporters gene orthologs, TcHMA2 and TcHMA3. Synteny analysis across diverse cacao genomes revealed structural variations and positive selection within the IB-2 HMA gene family. Expression pattern analysis demonstrated a high correlation between TcHMA2 and TcHMA3, suggesting low evolutionary divergence. The comparative analysis between T. cacao and Arabidopsis thaliana HMA genes revealed evolutionary divergence and sub-functionalization A. thaliana. Chapter III describes the functional characterization of cacao candidate genes TcHMA2 and TcHMA3 in yeast, a heterologous system, resulting in reduced yeast growth rates, an indirect effect of the import of Cd to the yeast cytosol. TcHMA2 has a truncated iv C-terminal domain and demonstrated lower Cd transport efficiency than the full-length TcHMA3 gene. Chapter IV includes the results of a collaborative study between Penn State and the Colombian Agricultural Research Corporation (AGROSAVIA), Colombia. The study characterizes the transcriptional responses to Cd treatment in leaf and root tissues from two cacao genotypes: PA121 (a high-Cd accumulator) and TSH660 (a low-Cd accumulator). Seedlings from these genotypes were exposed to Cd at 10 PPM for 48 hours. Total mRNA from leaves and roots was extracted and sequenced, and differential gene expression analysis was conducted. The study identified thousands of differentially expressed genes (DEGs) after 48 hours of Cd exposure: 4185 in roots and 2396 in leaves. Key pathways were significantly regulated, including ion transport, water stress, carbohydrate metabolism, pathogen response, and the biosynthesis of plant growth hormones such as abscisic acid (ABA), ethylene, indole-3-acetic acid (IAA), and melatonin. Based on the results from the transcriptome study, a working model for the Cd response in cacao was developed. To test the predicted model, open-pollinated seedlings of PA121 were grown in greenhouse conditions and exposed to Cd. The physiological response was evaluated after 36 hours of Cd treatment. Results indicated cacao plants treated with Cd had a significant reduction in leaf stomatal conductance, correlating gene expression changes in the ABA pathway to physiological outcomes. This study provides comprehensive insights into the evolution and functions of HMA genes in cacao. It also offers valuable information related to the molecular and physiological responses of cacao plants to Cd exposure. Together, this work contributes significantly to the body of knowledge on abiotic stress and provides significant insights on heavy metal uptake in cacao.