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The population structures of the zooxanthellate corals Acropora palmata and A. cervi- cornis were used as a proxy to estimate genetic connectivity between reefs of Puerto Rico. Sequences of the mitochondrial control region were recovered from geographically adjacent and distant reefs inhabited by A. palmata (n = 220) and A. cervicornis (n = 124). Both species exhibited low levels of mitochondrial nucleotide diversity, a common observation for scleractinian corals. Analysis of molec- ular variance based on coral colonies collected from 26 reefs of 6 localities suggested that significant population structure exists even between neighboring reefs (A. palmata, ΦST = 0.0863, p < 0.00098; A. cervicornis, ΦST = 0.1237, p < 0.00587). When all samples from Puerto Rico were combined and compared to samples from Lee Stocking Island, Bahamas, the pairwise genetic distances were also significant. Evidence for population structure in A. cervicornis was much stronger when introgressed and native alleles were used in combination rather than alone: A. cervicornis from Mona Island was significantly different compared to La Parguera and the Bahamas, but not to Desecheo Island. Recov- ery of Acropora in ecological time might rely on the survival and sexual reproduction of local popu- lations rather than replenishment from distant reefs because of the population subdivision observed at fine geographic scales.

No two reefs are created equal: fine-scale population structure in the threatened coral species Acropora palmata and A. cervicornis