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In the past, identification of the genus Kobresia was mostly dependent on morphological characteristics. This study used random amplified polymorphic DNA (RAPD), sequences of nrDNA ITS, cpDNA trnT-L-F spacer and cpDNA ndhF to assess the phylogenetic relationships among the accessions of Kobresia plants collected from the Tibetan plateau. In the dendrograms, Kobresia macrentha (L) species formed a separate clade suggesting a remote relationship with other accessions. These trees showed that species found in similar habitats or having similar adaptations tended to cluster together. Thus, the genetic variation and adaptation seen in these Kobresia accessions may be due to their remote geographic and high altitudinal position in the Tibetan plateau. This study highlights the importance of molecular analysis in understanding the genetic diversity and structure of Kobresia accessions, and contributes to the knowledge of conservation of genetic resources.