The orchid genus Caladenia is species rich with many threatened and endangered taxa. We report on the isolation and characterization of microsatellite loci in the rare Caladenia huegelii for molecular evaluation of this and the closely related C. thinicola as part of the development of conservation initiatives. Eight di- and trinucleotide loci were screened using 30 samples from each species. All loci were highly variable, with similar levels of heterozygosity and number of alleles across both species. These markers will be highly informative for population studies in both species.