Pigmented rice is reported have high levels of bioactive compounds, it suitable for functional food. Additionally, it has been reported that pigmented rice extract has the potential as an anti-obesity, anti-inflammatory, antioxidant, and anti-cancer agent. In Indonesia, pigmented rice is less favored by local farmers due to low public demand (limited awareness) and cultivation difficulties (prone to falling and susceptible to pests), which could lead to the extinction of the plant. Qualitative and quantitative characterization can serve as the basis for plant breeding. This study aims to analyze the morpho-agronomic traits of several pigmented rice accessions from Central Java and East Java, thus providing a source of information for local farmers in the pigmented rice breeding process. Morpho-agronomic traits observed include qualitative and quantitative characters. The grouping and its relationship between 22 rice accessions were analyzed using Principal Component Analysis (PCA)-biplots and dendrogram clustering analysis based on Unweighted Pair Group Method Using Arithmetic Averages (UPGMA). The results showed the characteristics influencing the variation of Indonesian pigmented rice, especially from East Java and Central Java, out of 22 accessions, such as leaf color, shoot color, and tiller number. The grouping based on their morpho-agronomic characters showed that there were two main clusters. Twenty out of 22 rice accession grouping in cluster 1 with diverse pigmented rice pigment type. Meanwhile, cluster 2 consists of IR Ngawi Hitam and Wojaloka. These two accessions are classified as black rice. Our findings are valuable for breeding programs, especially in rice.