Dinoflagellates of the genus Symbiodinium form symbioses with a variety of animal and protistan hosts, including reef-building corals. Growing concern about the global degradation of coral reefs has underscored the need to understand these complex symbiotic relationships. This dissertation documents the extent to which corals and other symbiotic cnidarians show fluctuations in their associations with Symbiodinium spp. The presence of free-living Symbiodinium and the onset of symbiosis in juvenile hosts were investigated using aposymbiotic scyphistomae of the jellyfish Cassiopea xamachana. Scyphistomae exposed to various habitats took a variety of distinctive symbionts into symbiosis including members of sub-generic clades A, B, C and D. Adult C. xamachana possessed only Symbiodinium type A1 implying that specificity likely develops as a result of post-infection processes due to competitive exclusion or other mechanisms. The genetic identity of Symbiodinium was examined seasonally in six species of broadcast spawning corals (Acropora palmata, A. cervicornis, Siderastrea siderea, Montastrea faveolata, M. annularis, and M. franksi) from the Bahamas and Florida Keys. Most coral colonies showed little to no change in their dominant symbiont. However, certain colonies of M. annularis and M. franksi from the Florida Keys exhibited significant shifts in their associations attributed to recovery from the stresses of the 1997-98 El Nio Southern Oscillation (ENSO) event. Intracolonial shifts of mixed Symbiodinium populations were also examined for colonies of M. annularis from Florida. To test whether mode of symbiont acquisition influences the stability of coral-dinoflagellate symbioses, three species of brooding coral species (Agaricia agaricites, Porites astreoides, and S. radians) were examined seasonally for several years. Symbiotic associations in all brooding colonies did not vary, suggesting that reproductive mode has a significant effect on the stability of these symbioses. Finally, the physiology of the host-symbiont association (holobiont) was examined in colonies of M. annularis which harboring different Symbiodinium communities. Colonies harboring populations of mixed symbiont types, including the putatively stress tolerant type D1a Symbiodinium, had significantly different zooxanthellae densities, photosynthetic capacity of PSII and host tissue biomass than colonies harboring exclusively type B1. After type D1a was displaced, no significant differences were detected, suggesting that the identity of Symbiodinium harbored significantly effects the physiology of the holobiont.