<p>Genetic diversity of rice, based on its agronomical traits and nutritional content, has become valuable for improving breeding. Gamma-aminobutyric acid (GABA) is an amino acid naturally present in considerable amounts in rice grains and has excellent health benefits. However, the rice germplasm’s utility to breeding programs, particularly in local Indonesian rice, is limited by a lack of reliable germplasm characterization data. This study aimed to evaluate the genetic diversity of 20 Indonesian rice germplasms and assess the significant associations between simple sequence repeat (SSR) markers and agronomic traits and GABA content. A randomized complete block design with three replications estimated genetic diversity parameters. Genetic diversity analysis revealed significant variations, high genotypic coefficient variations, and medium-to-high heritability in agronomical traits. Correlation and path analyses generally revealed that the days to maturity, number of productive tillers, panicle length, plant height, and grain width can be used as agronomic markers for selecting rice genotypes with high GABA content. Genotypes were categorized via cluster analysis based on agronomic traits and SSR markers into two main clusters. Padi Huma formed a cluster at the farthest distance and had the highest thousand-grain weight among the genotypes. Association analysis revealed that a single marker was associated with multiple traits and vice versa. RM1376 was the most strongly associated with GABA content, indicating the potential for accelerating marker-assisted breeding to improve GABA content.</p>