Genome reduction followed by 454 DNA sequencing was previously described in three orphaned Andean crops: grain amaranth or kiwicha (Amaranthus caudatus, 2n=2x=32); papalisa (Ullucus tuberosus, 2n=2x=24); and oca (Oxalis tuberosa, 2n=8x=). Kiwicha is an ideal subsistence crop for intermediate-altitude tropical and subtropical environments due to its superb nutritional characteristics and culinary versatility. Papalisa and oca are starchy tuber crops that fill a vital agronomic niche in highland potato production systems. These sequences were mined for potentially useful SNP and SSR markers. We herein discuss the use of these markers for diversity studies in Peruvian collections of kiwicha and oca. Most notably, Fluidigm-based SNP assays in kiwicha identified that a cryptic vitreous-seeded type of kiwicha derived from unintentional hybridization with black-seeded wild amaranths has been under selection in multiple areas of the central Andes.