Zingiber moran, a rare ginger found only in a few parts of northeast India, faces the threat of extinction due to its exploitation
as an important medicinal plant. In this study, the chromosome number of wild ecotypes of Z. moran was determined and the
genetic analysis was carried out using two kinds of molecular markers: inter simple sequence repeats (ISSR) and amplified
fragment length polymorphism (AFLP). A chromosome number of 2n ¼ 22 was confirmed for all 10 ecotypes investigated.
AFLP analysis revealed a greater amount of genetic polymorphism (95.06%), with a strong resolving power in detecting
intraspecific variation, compared to ISSR analysis (34.61%). Genetic diversity parameters, such as number of observed
alleles (na), mean number of effective alleles (ne), mean Nei’s gene diversity index (h), and Shannon index (I) for ISSR and
AFLP were in the range 1.34–1.95, 1.25–1.60, 1.44–0.33, and 0.20–0.49, respectively. Marker indices and polymorphic
information content varied from 0.5–19.3 and 0.03–0.27 for ISSR, and 28.2–39 and 0.3–0.39 for AFLP, respectively.
Dendrograms derived by unweighted pair group method of arithmetic averages cluster analysis based on molecular data
classified the ecotypes into two major clusters. The Mantel test cophenetic correlation coefficient (r) for ISSR (0.85) and
AFLP (0.91) showed a good degree of confidence in the association with 10 ecotypes. Clustering was further supported by
principle component analysis which demarcated individuals of hilly topography from the ones of plain land.