The accurate identification of germplasm accessions is the prerequisite and basis for the diversity research on seed industry and industrialization development in quinoa（Chenopodium quinoa Willd.）. In this study，the multiple PCR amplicon capture technology（MultipSeq）was adopted to obtain 656 SNPs used for the genetic diversity analysis of 251 quinoa germplasm accessions，and perl scripts were adopted to construct DNA fingerprints of each accession and personal ID cards were constructed based on the fingerprint information. The analysis of the population genetic structure showed that 251 germplasm accessions were divided into two subgroups Ⅰ and Ⅱ，corresponding to the Andean high-altitude quinoa groups and the Chilean low-altitude quinoa groups. The Ⅰ and Ⅱ population genetic diversity index（π values）were 0.0037 and 0.0036，respectively. The population differentiation index（Fst value） is 0.14. The results of the population principal component analysis are completely consistent with the results of population genetic structure，and there are some genetic crossovers between subgroups. Phylogenetic analysis shows that Ⅰ group includes 152 germplasm accessions mainly from Bolivia and Peru，and Ⅱ group includes 99 germplasm accessions mainly from Chile. TheⅠgroup is further divided into two subgroups Ⅰ-1 and Ⅰ-2. The Nei′s genetic distance between Ⅰ-1 and Ⅰ-2 was 0.054. Among the 112 germplasm accessions from Shijiazhuang（Hebei），40，24 and 48 accessions were closely related to the Bolivian，Peruvian and Chilean germplasm in kinship relationship，respectively. The construction of molecular ID among 251 germplasm accessions could play an important role to trace and protect the quinoa germplasm in this study. The results of population genetic diversity analysis have certain reference significance for the classification and systematic arrangement in quinoa germplasm in China.