Nepal has a wide diversity of rice landraces in all rice-growing areas from low to high altitude. A baseline survey in Jumla, a
high-altitude site (2200–3000 m), identified rice landraces with different names that differed in phenotype and were adapted to
the extreme high-altitude environment. Jumli Marshi was the most common traditional rice variety, accounting for 85% of
samples collected. The genetic diversity of these landraces was assessed by agro-morphological variability and microsatellite
marker polymorphism. Forty-two qualitative and quantitative traits and 39 microsatellite (simple sequence repeats, SSR)
markers were assessed among accessions with 10 different names. The accessions showed low morphological diversity with an
average Shannon Weaver diversity index of 0.23. Only 16 morphological traits showed significant variation among the
accessions. Discriminant function analysis showed that only 36% of accessions could be clustered according to name by
morphological traits. Only one SSR locus was polymorphic, distinguishing only one accession. The names used by farmers to
describe the phenotypic characteristics of panicle and grains were inconsistent indicators of genetic identity. We conclude that
the Jumla landrace population has a narrow genetic base. The diversity detected was sufficiently low for it to be possible that
there was a single origin for all of the Jumla landraces.