The Caribbean Basin harbors a significant amount of biodiversity yet few studies have reported the genetic diversity of species endemic to this region. Knowledge of a species population-wide genetic makeup is vital to formulate successful conservation strategies. Ipomoea microdactyla Griseb. (Convolvulaceae) is a hermaphroditic, self-incompatible vine occurring in Miami-Dade County, Florida (USA), the Bahamas, and Cuba. This species is listed as endangered in the state of Florida. Presently most Floridian populations are restricted to small habitat fragments while Andros Island (the Bahamas) populations are found in the largest expanse of continuous pine forest remaining in the Caribbean Basin. The purpose of this project is to compare the genetic diversity and population genetic structure of populations in Miami-Dade County and on Andros Island, the Bahamas for conservation management. Microsatellite genetic markers originally developed for Ipomoea batatas (sweet potato) were utilized for this study. Overall genetic diversity was relatively high for both Floridian and Androsian populations. Alleles restricted to each region were found. Most genetic variation is found within populations rather than among populations as theory predicts for self-incompatible species. However the AMOVA test shows significant population differentiation both among populations within regions (FST = 0.167, p < 0.01) and among populations between regions (FRT = 0.093, p < 0.01). For the eight loci used, there is evidence of inbreeding as most values of FIS are positive. All remaining isolated Florida populations may be required to maintain the genetic diversity and fitness of this endangered vine in the United States.