Metal Tolerance Proteins (MTPs) are the class of membrane proteins involved in the transport of metals, mainly Zn, Mn, Fe, Cd, Co and Ni, and confer metal tolerance in plants. In the present study, a comprehensive molecular analysis of rice MTP genes was performed to understand the evolution, distribution and expression dynamics of MTP genes. Exploration of the whole genome re-sequencing information available for three thousand rice genotypes highlighted the evolution and allelic diversity of MTP genes. Based on the presence of non-synonymous single nucleotide polymorphism (SNP), MTP1, MTP6, MTP8 and MTP9 were found to be the most conserved genes. Furthermore, results showed localization of MTP1, MTP8.1 and MTP9, and MTP11, respectively with QTLs/m-QTLs for Zn and Cd accumulation, making these genes promising candidates to understand the QTL regulation. Expression profiling of the entire set of 10 MTP genes revealed root and shoot specific expressions of MTP9 and MTP8.1, respectively, under all tested vegetative stages. Expression of seed-specific MTPs increased as seed maturation progressed, which revealed their potential role in transporting metals during seed filling. Upon exposure to harmful heavy metals, expression of most MTP genes decreased in root and increased in shoot, suggests that different mechanisms are being employed by MTPs in different tissues. Contrastingly, only a few MTPs were found to be responsive to Fe and/or Zn starvation conditions. The extensive analysis of MTPs presented here will be helpful in identifying candidate MTP genes for crop biofortification and bioremediation purposes.