Zokor (Mysopalacinae) is a group of subterranean rodents. Although they are regarded as important components in the ecosystems they belong to, due to their underground lifestyle, very little is known about their ecology and behavior. Development of microsatellite markers can potentially assist in addressing behavioral and ecological questions such as dispersal, mating and social systems. Here we report the development of 11 polymorphic microsatellite loci from the genome of Eospalax cansus using 454 shot-gun sequencing. Genetic diversity was assessed using DNA samples of 47 individuals of E. cansus from a single location. Cross-amplification in Eospalax baileyi was also tested, with five polymorphic markers being amplified successfully. These markers are the first published microsatellites loci from E. cansus and will be invaluable for studies addressing ecological and behavioral questions involving E. cansus and E. baileyi, and potentially other species in Mysopalacinae.