Rice landraces have been developed through artificial selection imposed by farmers during the long-term domestication process. Although the global rice diversity is well characterized, few studies have conducted an in-depth analysis of genetic diversity on a local scale. In India, there are many locally adapted non-Basmati aromatic rice landraces in which the pace of improvement is slow, despite their high economic values. The aromatic and quality rice landraces of Manipur, locally called Chakhao (delicious), are important, considering their high economic and cultural values. To conserve and encourage improvement of these landraces, we collected Chakhao accessions from eight districts of Manipur. The aim of the current study was to investigate the level of genetic diversity and structure of 37 Chakhao landraces based on genotyping with 47 microsatellite markers. The genetic diversity analysis revealed high gene diversity (0.673) within the Chakhao population, with values ranging from 0.303 (Poireiton) to 0.471 (mixed Chakhao). The Chakhao rice accessions could be divided into six subgroups based on genetic structure analyses. The population structure derived from the STRUCTURE analysis largely correlated with the farmers' classification of Chakhao landraces. The results of genetic diversity analyses and the indigenous knowledge of the names and use of Chakhao landraces would facilitate the conservation and utilization of this unique genetic resource.