Micronutrient deficiencies, notably zinc (Zn) and iron (Fe), affect approximately two billion people worldwide, significantly burdening developing countries. Diets predominantly based on rice, which sustains over 90 % of the Asian population, are frequently deficient in these essential micronutrients. This investigation evaluated the zinc concentration in milled rice (MR) across 90 Advanced Breeding Lines (ABLs), revealing a substantial variation in zinc content ranging from 13.7 to 33.80 ppm. A GWAS using the FarmCPU model effectively controlled for population structure and kinship, revealing genetic loci associated with zinc concentration in rice grains. The analysis uncovered 11 significant marker-trait associations (MTAs) related to zinc content, with several MTAs co-localizing with known zinc-associated traits, suggesting the potential for simultaneous enhancement of these traits. These robust MTAs present valuable targets for biofortification strategies aimed at increasing the zinc content in rice grains, thereby contributing to the mitigation of zinc deficiency among rice consumers. The 11 identified MTAs for Zn traits can fast-track marker-assisted breeding for developing zinc-enriched rice varieties. These findings are pivotal for ongoing initiatives to address micronutrient malnutrition and improve the nutritional quality of rice. Additionally, these MTAs facilitate gene pyramiding and genomic selection to boost breeding precision and efficiency.