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Orbicella annularis (Ellis and Solander, 1786), a key reef building species, is unusual among Caribbean corals in the flexibility it displays in its symbioses with dinoflagellates in the family Symbiodiniaceae. This variability has been documented at a range of spatial scales; from within and between colonies to scales spanning the entire species range. However, temporal variability in Symbiodiniaceae communities found within O. annularis colonies is not well understood. Evidence suggests that symbiont communities in this coral species fluctuate temporally in response to environmental stressors (sporadic changes in abundance and in community composition). In this study, we investigated temporal stability of symbiont communities in O. annularis at four sites in The Bahamas over a period spanning 6 yrs. While the dominant symbiont species, Breviolum minutum (LaJeunesse et al.) J.E.Parkinson & LaJeunesse (formerly ITS2-type B1), remained stable across four patch-reef study sites, finer resolution molecular techniques revealed inter-annual variability in the presence/ absence of cryptic species Durusdinium trenchii (LaJeunesse) LaJeunesse (formerly ITS2-type D1a). Durusdinium trenchii is known to play a role in resistance to environmental stress and may have a protective effect under warm conditions. These results suggest that, while it might take an extreme environmental perturbation to trigger a long-term shift in the dominant symbiont, at background levels, less prevalent symbiont taxa are likely to be continually shuffling their relative abundances as they change in response to seasonal or environmental changes.