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Due to its nutritional content and beneficial health, black and red rice, which belong to pigmented rice, has become more popular. Research on pigmented rice in Indonesia has not been intensively carried out, so information on the genetic diversity of pigmented rice is very important for an effective breeding program. This research was conducted to analyze the genetic diversity of 15 accessions of local pigmented rice collected from Eastern Indonesia (Sulawesi and East Nusa Tenggara) in IAARD-ICABIOGRAD Gene Bank based on 33 morpho-agronomical characters and 24 SSR markers. The experiment was designed in a randomized complete block design with three replications. The morpho-agronomical observation was performed based on a standard descriptor for rice. The morpho-agronomic characters of all observed accessions varied, indicating high diversity. Based on the characteristic of SSR markers, the average allele number, major allele frequency, gene diversity, heterozygosity, and the PIC were 4.88, 0.47, 0.66, 0.02, and 0.62, respectively. The similarity coefficient between accessions based on morpho-agronomic characters and SSR markers was still quite high (80%). PCoA and phylogenetic analyses based on the results of combined SSR and morpho-agronomic data formed three different groups at a cophenetic distance of 0.22. The result of this study is expected to provide a better understanding of the genetic characteristics of the accessions for further use to support the PGR breeding program. [ABSTRACT FROM AUTHOR]