The antagonistic effect between mercury (Hg) and selenium (Se) is conclusively established in animals and human beings in the past decades. However, the underlying mechanisms of the interactions between Hg and Se in plants, as well as the metabolism of Hg-Se compounds in crops are still far from being understood. The botanic metallomics of Hg and Se mainly focuses on the translocation, transformation, and metabolism of Hg and Se in the environmental and botanic systems employing metallomics methods. An adequate understanding of the biological behavior of Hg and Se in plant is beneficial for sequestration of Hg and Se in soil-plant systems with high Hg and Se contamination. It can also provide a molecular mechanistic basis for Se supplementation in Se-deficient areas. Here, the key developments in current understanding of Hg and Se interactions in plants are reviewed. The metabolism and antagonism of Hg and Se in various plants, as well as the advanced analytical methods commonly used in this field, are summarized and discussed. As suggested, plant Hg and Se uptake, metabolism, and antagonism can be taken into account for detoxification and remediation strategies for the reduction of Hg and Se in the food chain.