The grain amaranths (Amaranthus hypochondriacus L., A. cruentus L., and A. caudatus L.) are important pseudo‐cereals native to the Americas. The objective of this project was to produce and characterize a set of highly informative, reproducible microsatellite markers for the grain amaranths. A total of 1457 clones were sequenced from three microsatellite‐enriched libraries. Of these, 353 contained unique microsatellites. An additional 29 microsatellite loci were identified from 728 bacterial artificial chromosome–end sequences. A total of 179 microsatellites were polymorphic across accessions from the three grain amaranths. Among these polymorphic microsatellite loci, a total of 731 alleles were identified with an average of four alleles per locus. Heterozygosity values ranged from 0.14 to 0.83, with a mean value of 0.62. Thirty‐seven (21%) of the markers were polymorphic between the parents of a segregating population. Phylogenetic analysis using the marker data placed A. hybridus L. accessions into two of the three grain amaranth clades, suggesting the polyphyletic evolution of the three cultivated species from different A. hybridus ancestors. The transferability of these markers to A. hybridus, A. powellii S. Wats., and A. retroflexus L. is reported and suggests that these markers may be useful in studying other species within the genus Amaranthus, including several economically important weeds and ornamentals.