Quinoa is an important staple food crop for millions of impoverished rural inhabitants of the Andean region. Quinoa is considered a good source of protein,vitamins, minerals, and antioxidants. This study aimed to investigate the genetic diversity and population structure of world quinoa gennplasm originating from 8 countries through the iPBS-retrotransposon marker system. Molecular characterization was performed using the 11 most polymorphic primers. A total of 235 bands were recorded, of which 66.8% were polymorphic. Mean polymorphism information content (PIC) was 0.410. Various diversity indices including mean effective number of alleles (1.269), mean Shannon's information index (0.160) and gene diversity (0.247) revealed the existence of sufficient amount of genetic diversity in studied germplasm. Bolivia-17 and Mexico-1 were found to be genetically distinct accessions and can be suggested as candidate parents for future breeding activities. Various diversity indices were also calculated among germplasm collection counries and the results clearly showed the existence of higher genetic diversity in Bolivian and Peruvian accessions. The model-based structure, neighbor-joining, and principal coordinate analysis (PCoA) grouped quinoa germplasm according to their collection country. Analysis of molecular variance (AMOVA) revealed that most of the variations (69%) in world quinoa germplasm are due to differences within populations. Findings of this study can be used for deeper understanding of the genetic relationship and in the determination of appropriate breeding and conservation strategies for quinoa.