Rice is a staple food crop comprising two main subspecies, indica and japonica, which have diverged through adaptation and domestication. While recent genome assemblies provide high-quality references, a single reference genome cannot capture the full extent of genetic variation in rice. A pangenome constructed from multiple individuals can overcome the limitations of using a single reference genome. In this study, the first Vietnamese rice pangenome was constructed using 20 rice landrace accessions and the IRGSP-1.0 reference genome. The pangenome was constructed using an iterative mapping and assembly approach, spanning 386.89 Mb, and included 13.64 Mb of novel sequences specific to Vietnamese landraces. Genome annotation identified 37,292 genes, including 33,710 core, 3,560 dispensable, and 22 unique genes. Among these, 3,116 genes were variably present across both indica and japonica groups but were not conserved within either group. From this set of shared variable genes, 122 genes were linked to important agronomic traits. Genes related to auxin and chlorophyll content included OsMKK6, OsMEK1, OsDLT10, OsPYL10, OsPYL3, and OsRCAR1. Genes involved in photosynthesis and transpiration included REL2, OsDLT10, and RSD1. Floral development was associated with OsbZIP47, while OsBOP3 and OsBSK3 contributed to inflorescence traits. Root development involved OsNAC2, OsCSLC7, OsMKK6, and OsMEK1. Grain length, shape, number, and weight were associated with key genes such as OsBSK3, OsCDKF2, REL2, OsJAZ10, OsTIFY11b, and OsWRKY19. Disease resistance genes were also identified, including OsCEBiP, Pikp1, Pikm5NP, xa47, and OsREM20. These shared variable genes provide valuable genetic resources for future rice improvement and breeding efforts.