The Eastern Himalayan region of Northeast (NE) India is home to a large number of indigenous rice varieties, which
may serve as a valuable genetic resource for future crop improvement to meet the ever-increasing demand for
food production. However, these varieties are rapidly being lost due to changes in land-use and agricultural
practices, which favor agronomically improved varieties. A detailed understanding of the genetic structure and
diversity of indigenous rice varieties is crucial for efficient utilization of rice genetic resources and for developing
suitable conservation strategies. To explore the genetic structure and diversity of rice varieties in NE India, we
genotyped 300 individuals of 24 indigenous rice varieties representing sali, boro, jum and glutinous types, 5
agronomically improved varieties, and one wild rice species (O. rufipogon) using seven SSR markers. A total of 85
alleles and a very high level of gene diversity (0.776) were detected among the indigenous rice varieties of the
region. Considerable level of genetic variation was found within indigenous varieties whereas improved varieties
were monoporphic across all loci. The comparison of genetic diversity among different types of rice revealed that
sali type possessed the highest gene diversity (0.747) followed by jum (0.627), glutinous (0.602) and boro (0.596)
types of indigenous rice varieties, while the lowest diversity was detected in agronomically improved varieties
(0.459). The AMOVA results showed that 66% of the variation was distributed among varieties indicating a very high
level of genetic differentiation in rice varieties in the region. Two major genetically defined clusters corresponding
to indica and japonica groups were detected in rice varieties of the region. Overall, traditionally cultivated
indigenous rice varieties in NE India showed high levels of genetic diversity comparable to levels of genetic
diversity reported from wild rice populations in various parts of the world. The efforts for conservation of rice
germplasm in NE India should consider saving rice varieties representing different types with specific emphasis
given to sali and jum types. The protection against the loss of vast genetic diversity found in indigenous rice
varieties in NE India is crucial for maintaining future food security in the changing world.