Abstract Coral reef conservation management policy often focuses on larval retention and recruitment of marine fish with scant data available on important, less motile reef-building species such as corals. To evaluate the concept of population connectivity in corals, we tested whether broadcast spawning reproduction per se confers the same degree of dispersal to two sister species, Montastraea annularis (Anthozoa: Scleractinia; Ellis and Solander 1786) and M. faveolata (Ellis and Solander 1786), both dominant taxa in reefs of the northern Caribbean. Genetic analyses of ten nuclear DNA loci (seven microsatellite and three single-copy RFLP) reveal strikingly different patterns of popula- tion genetic subdivision for these closely related, sympatric species, in spite of likely identical dispersal abilities. Strong population genetic structure typified the architecture of M. annularis, whereas M. faveolata populations were principally genetically well mixed. A higher level of clonality was observed in M. annularis potentially because of a susceptibility to physical fragmentation. Clonality did not, however, significantly contribute to population genetic structure or low-level Hardy–Weinberg and linkage disequilibria observed in some populations. The lack of consistent association between reproductive mode and dispersal reinforces the perspective that population connectivity is not so much a function of predictable marine population source and sink relationships as is due to a more complex interface of oceanic currents interacting with and amplifying stochastic fluctuations in larval supply and settlement success. Our results support others promoting an overall ecosystem approach in marine protected area design. Introduction Stony corals are the foundation of highly diverse marine ecosystems, providing structure, habitat, and primary productivity over vast areas of tropical near- shore habitat. Globally, many coral reef ecosystems are on a declining trajectory, as bleaching, disease, pollu- tion, siltation from terrestrial run-off, fishing, and a variety of other natural and anthropogenic pressures, singly and in combination, take their toll (Gardner et al. 2003; Pandolfi et al. 2003; Bellwood et al. 2004; Jones et al. 2004). Degradation frequently is noted for Caribbean coral reefs (Hughes 1994; Hughes and Tanner 2000; Gardner et al. 2003) with a growing indication that the Great Barrier Reef system of Communicated by S. Nishida, Tokyo Electronic Supplementary Material Supplementary material is available for this article at http://dx.doi.org/10.1007/s00227-006- 0332-2 and is accessible for authorized users. E. G. Severance Æ S. A. Karl Department of Biology, SCA 110, University of South Florida, Tampa, FL 33620-5200, USA Present address: E. G. Severance Stanley Division, Johns Hopkins University, 600 N. Wolfe Street, Blalock 1105, Baltimore, MD 21287-4933, USA Present address: S. A. Karl (&) The Hawai’i Institute of Marine Biology, University of Hawai’i, Manoa, PO Box 1346, Kaneohe, HI 96744, USA e-mail: skarl@hawaii.edu Mar Biol (2006) 150:57–68 DOI 10.1007/s00227-006-0332-2 123 RESEARCH ARTICLE Contrasting population genetic structures of sympatric, mass-spawning Caribbean corals Emily G. Severance Æ Stephen A. Karl Received: 27 February 2006 / Accepted: 15 April 2006 / Published online: 30 May 2006 Ó Springer-Verlag 2006