Deeringothamnus rugelii (Annonaceae) is a federally threatened shrub endemic to Volusia County, Florida. The species is historically known from 29 populations, which are threatened by development and habitat degradation. Only a few sites are protected, and the proportion of the total genetic diversity protected in these sites is unknown. D. rugelli may also be threatened by the loss of genetic integrity through hybridization with the more widespread, co-occurring close relative, Asimina pygmaea, and another rare congener, Deeringothamnus pulchellus. In this study, we asked the following questions: 1) Are D. rugelii, A. pygmea, and D. pulchellus genetically distinct? 2) Is there genetic evidence for interspecific hybridization between these species? And 3) What are patterns of genetic diversity and structure within D.rugelii and what are implications for conservation? Analyses of genetic structure indicated that most individuals of D. rugelii, A. pygmea, and D. pulchellus formed cohesive genetic groups, but some individuals were assigned to more than one genetic cluster, indicating that they are likely the products of hybridization. Most putative hybrids were crosses between D. rugelii and D. puchellus, with evidence of backcrossing with the parental species. We observed F1 hybrids between A. pygmaea and D. rugelii in sites where they co-occurred, with no sign of backcrossing, suggesting that hybrids may be sterile. D. rugelii shows high levels of genetic diversity, with most variation partitioned within populations, indicating high levels of intraspecific gene flow among populations. Because most variation of D. rugelii is partitioned within populations, only a subset of populations across the range of the species needs to be protected to conserve most of the genetic variation in the species. Given the populations that are already publicly protected, results indicate that the majority of the genetic diversity in the species is already protected. Thus, current conservation efforts are sufficient to protect the extant genetic diversity in D. rugelii, and future efforts should instead focus on maintaining good quality habitat to help support large populations of D. rugelli. Resutls were also used to select genetically appropriate germplasm for population introductions and to help determine whather to mix population sources into introduced populations.