Fine scale genetic structure of the coral Acropora palmata was investigated by sampling 9 reefs in Puerto Rico and 1 in the Bahamas as an out-group. Of a total of 276 samples, 201 had unique genotypes and the remaining 75 were clones. 48 of these unique samples representing 4 reefs were also profiled for mitochondrial haplotypes, resulting in 12 unique mitochondrial haplotypes. The analyzed samples originated from one panmictic populations, rejecting the hypothesis of eastern and western populations of A. palmata. AMOVA analyses also indicated that <1% of the variance in allelic frequencies was explained by differences between sampling localities. Genetic diversity was surprisingly high considering the observed demographic declines.