Biological self-recognition phenomena, analogous in many respects to vertebrate histocompatibility, are apparently widespread in scleractinian corals. Here we exploit the operational properties of a self-recognition bioassay to estimate clonal diversity and population structure in a common reef-building coral, Acropora cervicornis. When branches of A. cervicornis come into contact, within several months the tissues and calcareous matrix exhibit either an acceptance or rejection response. Through a variety of controlled experimental grafts, and observations of natural interactions, we demonstrate that these responses accurately distinguish clonemates (the products of asexual fragmentation of colonies) from non-clonemates (the products of sexual recruitment). This self-recognition bioassay was subsequently used to analyze the clonal structure and diversity in A. cervicornis populations in Discovery Bay. Jamaica, and Tague Bay, St. Croix, U.S. Virgin Islands. A total of nearly 500 experimental grafts was scored in situ and additional information was obtained from observations of naturally occurring contacts. In comparison to the Tague Bay population, the Discovery Bay population has a significantly greater microgeographic clonal diversity that is reflected in a much higher Neighbor Index, the proportion of rejection responses in contacts among adjacent colonies. In Tague Bay, spatial maps of A. cervicornis clones were constructed; they show that clones are variable in size (from a single colony to assemblages up to 10 m or more in diameter), and are distributed in discrete patches. A computer model was used to simulate the development of clonal population structure from simple demographic processes (colony mortality, asexual and sexual recruitment). Using empirically derived rate estimates of these demographic processes we found that the quantitative predictions of Neighbor Index values from the model corresponded closely to our bioassay estimates of this parameter for real populations. Qualitative predictions of the model were also in good agreement with our empirical assessments of the size range of an individual clone's spatial distribution in the Discovery Bay population, and the degree of segregation and variance in size observed for spatial distributions mapped in the Tague Bay population. The model indicated that the relatively low diversity of clones apparent in the Tague Bay population is expected when the input of new clones into the population by sexual recruitment is extremely low Recently settled Acropora colonies did in fact appear to be virtually absent in this population. Sedimentation on the Tague Bay reef may interfere with the establishment of juvenile scleractinia on the available substrata. The simulations also predict that occasions of catastrophic mortality and subsequent recovery of A. cervicornis populations may be major determinants of clonal diversity and population structure, especially when the rate of sexual recruitment is relatively low Major disturbances, such as severe hurricanes, may prevent populations of A. cervicornis from attaining equilibrium patterns of clonal structure.