Good quality rice properties are affected by consumers’ preferences, community culture, and postharvest procedure. Although we use a lot of non-glutinous rice for our life, glutinous rice also plays an important role in worldwide. In addition, to increase rice production for food security, non-photoperiod rice varieties have been growing in many countries. In the present study, we carried out Genome-wide association study (GWAS) for glutinous rice and improved rice varieties using a panel of 99 indica rice accessions from the Vietnamese Mekong Delta. A total of 16517 good quality SNPs, which was filtered from digest restriction-site associated DNA sequencing (ddRAD-seq) of 99 rice accessions, was used for performing phylogenetic tree, principal component analysis (PCA), and GWAS. Interestingly, the phylogenetic tree and PCA show that the genotypic traits of improved rice varieties were clearly distinguished from traditional rice accessions, while the genotypic traits of glutinous rice were also separated from non-glutinous rice, but it was not clear. Therefore, these SNPs (genotype) were performed GWAS for glutinous rice and improved rice varieties. We identified three good candidate chromosomes for glutinous rice (Chr01, Chr06, and Chr12), and five good candidate chromosomes for improved rice cultivars (Chr01, Chr04, Chr06, Chr08, and Chr11). The identified SNP markers for glutinous rice was 30 and 101 SNP markers for improved rice varieties. The research resulted that these SNP markers are valuable SNP candidates to detect candidate genes related to glutinous rice and improved rice varieties.