In order to study the genetic diversity and the genetic background of quinoa (Chenopodium quinoa Willd.) germplasms distributed in China, molecular markers research was carried out based on 163 quinoa accessions and 3 djulis (Chenopodium formosanum Koidz.) accessions by using 66 simple repeat sequence (SSR) markers, to analyze the polymorphism and inter-species relationship. According to the data, a total of 327 alleles were amplified from 66 SSR markers, with an average of 5.031 alleles per marker. The mean values of observed and expected heterozygosity were 0.387 and 0.588, respectively, while the mean values of the polymorphism information index was 0.524. The method of UPGMA clustered all the accessions into three groups. Group I included 3 djulis accessions only. Group II included 103 accessions, most of which were derived from USDA-NPGS and Chilean types. Group III included 60 accessions, most of which were derived from Bolivian and Peru types. The quinoa population was divided into two groups by population structure analysis and principal component analysis, and there was gene exchange between the two groups. The results indicate that there is a clear distinction between Bolivian, Peru accessions and American, Chilean accessions in genetic information, and the genetic relationship of the accessions from Qinghai and Yunnan are closer to Andean highland type, while the accessions from Hebei and Shanxi are closer to Chilean lowland type. Djulis is a native plant in Taiwan.