Because Cadmium (Cd) is harmful to humans, and most non-smokers are exposed to Cd mainly through rice consumption, low-Cd rice breeding is urgently needed. It might not be possible to apply variation created using gene editing technology to breeding directly, so it is important to explore genetic variation in this trait in a natural population. In this study, variation in 4 genes was identified among 3024 accessions from the International Rice Research Institute 3000 Rice Genome Project (IRRI 3K-RGP) and 71 other important varieties, and the relationships between the variants and plant Cd accumulation were validated with hydroponic and pot experiments. Variants in OsNRAMP1, OsNRAMP5, OsLCD, and OsHMA3 were grouped into two, four, three, and two haplotypes, respectively. Fourteen combinations of these haplotypes, which were referred to as Cd-mobile types, were found in the collection. Of these, type 14 was shown to have the greatest potential for low-Cd accumulation, and functional markers for this type were designed. The results of this study provide an important resource for low-Cd rice breeding and highlight an effective strategy for pre-breeding programs.