Rice is the staple food for more than half the world’s population. It is known that Zinc is one of the most important essential micronutrient for human About thirty percentage world’s population doesn’t still get enough zinc through their diets. As a staple food of over half world’s population, rice should take the responsibility to provide much more zinc in the future. Here, we performed Genome-Wide Association Study(GWAS) with high-resolution density SNPs and InDels to identify natural allelic variation in zinc increase from Heuristic or core rice set, which is derived from a total 24,368 rice germplasms. The range of the concentration and distribution of zinc in 137 core accessions of brown rice grain were wide, from 7.86ppm to 31.76ppm, with mean 18.97ppm. In particular, GWAS result show that the high peak found in Chromosomes (1, 4, 6, 8). The new natural variants identified through haplotyping analysis would be useful to develop new rice varieties with improved storage ability of the valuable mineral through the future molecular breeding.