Technical Abstract: Ipomoea microdactyla Griseb. (Convolvulaceae) is restricted to the Bahamian archipelago, Cuba, and southeastern Florida. The species is listed as endangered in U.S.A. where it is mostly restricted to the hyper-fragmented pine rockland of Miami-Dade County. Using seven DNA microsatellite loci, we assessed levels of genetic diversity for 12 populations of this species from Andros Island in the Bahamas (six sites), Cuba (one site), and Florida (five sites located in fragmented, pine rockland remnants). We found significantly greater mean numbers of alleles, and higher mean values for both observed and expected heterozygosity in populations from the continuous forest on Andros than those from the habitat fragments in Miami-Dade County. It is unknown if these patterns of genetic diversity in the Florida populations are the result of habitat fragmentation or founder effects. The population from Cuba exhibited relatively high levels of genetic variation suggesting that this island is a major center of diversity and dispersal for this species. It appears that hybrid introgression for I. carolina alleles within I. microdactyla individuals occurred at single site on Andros Island. Overall, the mean inbreeding coefficient value was 0.089 which suggests low levels of inbreeding. The highest inbreeding coefficient values were mostly recorded in Florida. The patterns of microsatellite variation have a clear geographical signature and this was supported by the clustering analyses. Two groups were revealed, one containing the populations from Florida, and the second one having those from the 38 Bahamas and Cuba.