In this study, we developed a new set of microsatellite markers for endangered Cattleya labiata and Cattleya warneri. Also the first microsatellite loci for Cattleya, these markers can be useful for studies in the conservation genetics of these species. Twenty-one new microsatellite primers pairs were characterized by cloning an enriched library, and two libraries were obtained by cloning inter-simple sequence repeats. Thirteen polymorphic primers were found, and the remaining eight were monomorphic for both species. Our results indicate that these new microsatellite markers have the potential to be used as a tool for studying the genetic diversity of C. labiata and C. warneri and for future studies focusing mating systems and the detection of hybrids.