The Greater Short-horned Lizard (Phrynosoma hernandesi) is a small reptile endemic to western North America that is classified as endangered in Canada. Here, we describe the development of 8 microsatellite markers for P. hernandesi. Observed allelic diversity varied from 2 to 11 while observed heterozygosity and expected heterozygosity ranged from 0.370-0.852 to 0.486-0.856, respectively. These markers will facilitate studies that address conservation of the species, such as levels of genetic diversity and population structure.