The orchids in the genus Chiloglottis are pollinated exclusively by sexual deception. We describe 20 variable microsatellite loci that will facilitate the study of the evolution and ecology of this specialized pollination system. Two loci were isolated from Chiloglottis trilabra, with the rest derived from Chiloglottis valida. All loci were polymorphic in C. valida (HE 0.07–0.87). Most loci amplified, and were variable within close relatives of C. valida, and a number amplified more broadly, including outside the genus.