Zinc and iron are essential mineral elements for the growth of Oryza sativa L. and also micronutrients for human health. Therefore, it is vital to study biofortification of rice with Zn and Fe in order to improve the yield and quality of rice, as well as to enhance nutritional states of humans. The zinc-regulated transporters and iron-regulated transporter-like proteins (the ZIP family) control the absorption and translocation of Zn and Fe and maintain their homeostasis in rice. Reciprocally, the expression of the ZIP family is induced by the concentration of Zn and Fe. There are abundant natural allelic variations of the ZIP genes, and some haplotypes only occur in indica or japonica, which could affect Zn and Fe accumulation levels between these subspecies. Currently, emerging functional studies of the accumulation mechanism of Zn and Fe in grains reveal that a lot still needs to be learned about the allele variations of ZIP genes. In fact, only OsZIP3 is functional characterized. In this review, we summarize the latest progress in the molecular characteristics of the ZIP transporters, including protein localization, gene expression patterns, transport mechanism, metal ion interaction, and natural allelic variations.