Harrisia portoricensis is a columnar cactus endemic to Puerto Rico. It was first collected and described from southern Puerto Rico, but urban and agricultural development extirpated these populations. At present, the species is restricted to the islands of Mona, Monito and Desecheo. In addition to its limited distribution, H. portoricensisis threatened by the activity of feral goats and pigs on two of these islands. These and other considerations motivated its inclusion in the U.S. Fish and Wildlife Service threatened and endangered species list (U.S. Fish and Wildlife Service 1990). Microsatellites or Simple Sequence Repeat (SSR) markers are being widely used in plants for a variety of applications including the assessment of the genetic diversity of natural populations. Microsatellites are typically highly polymorphic and robust, and also have a high level of transferability to related species (Varshney et al. 2005). The use of these markers could prove very useful for the study of genetic structure, gene flow and the degree of inbreeding in populations of Harrisia portoricensis. These analyses could in turn provide insights into the factors and processes that affect the survival of the species, information that will be valuable for formulation of effective management and conservation strategies.