Moringa belongs to the family Moringaceae comprising 13 species of which Moringa oleifera is more widely
cultivated. It is an economically important multipurpose tree with immense nutritional value and
has significant potential to address malnutrition. In the present study, a total of 97 accessions collected
from different districts of Tamil Nadu, Andhra Pradesh and Odisha were genotyped using 20 simple
sequence repeat (SSR) markers to assess the genetic diversity and population structure. A total of 140
alleles were detected with the polymorphic information content value of 0.6832 and gene diversity
0.7292. Population structure analysis through a model- based approach divided the accessions into two
subgroups. Molecular variance analysis using principal coordinate analysis (PCoA) summarized a 18.32%
variation in the first 3 axes and analysis of molecular variance analysis indicates a 2% variance among the
population with the remaining 98% variance attributed to variation within individuals. Cluster analysis
based on unweighted neighbour-joining showed a clear separation of samples into two subgroups. Further
comparison of the cluster subgroup showed high consistency with the STRUCTURE pattern and PCoA plot. The findings reveal a high diversity in the analysed genotypes from which a few distinct accessions could be utilized for further exploration based on their nutritional content and for conservation of nutritionally
superior germplasm.