Quinoa (Chenopodium quinoa Willd.) is an important seed crop in the Andean region of South America due to both its impressive nutritional quality and tolerance to drought and saline soils. We report the identification of single nucleotide polymorphisms (SNPs) using a genomic reduction protocol based on restriction site conservation and 454 pyrosequencing using eight diverse quinoa accessions. A total of 1,717,000 (436 Mb) sequence reads with an average read length of 255 bp were assembled into 45,751 contigs. The assembled contigs had an average length of 482 bp and read coverage of 23X and an average base coverage of 11X. A custom perl script (SNP_Finder) was used to identify 29,385 SNPs. We also report the development and characterization of 512 functional SNP marker assays. Assays are based on KASPar TM genotyping chemistry and were detected using the Fluidigm dynamic array platform. A diversity screen of 120 accessions was used to measure the information content of each marker. Two recombinant inbred mapping populations (0654 X KU-2’ and ‘0654 X NL-6’) were used to develop a consensus genetic linkage map of quinoa.