Clasping Warea (Warea amplexifolia) is a critically endangered plant species endemic to Florida. It is threatened due to habitat loss through urban development and poor land management, resulting in habitat fragmentation and small population sizes. To aid recovery strategies, information is needed on the genetic diversity among and within populations. We identified fourteen microsatellite loci that were polymorphic in W. amplexifolia and in the related W. sessilifolia, and nine loci that were polymorphic in W. cuneifolia. In W. amplexifolia, the number of alleles per microsatellite locus varied between four and 15, with observed heterozygosity in the range of 0.10 to 0.73. These newly identified markers will be used to inform recovery efforts for W. amplexifolia and may also be useful for studies of the population genetics of closely related taxa.