Considerable variability in bleaching was observed within and among soft coral taxa in the order Alcyonacea (Octocorallia: Cnidaria) on the central Great Barrier Reef (GBR, latitude 18.2°-19.0°S, longitude 146.4°-147.3°E) during the 1998 mass coral bleaching event. In April 1998, during a period of high sea surface temperatures, tissue samples were taken from bleached and unbleached colonies representative of 17 soft coral genera. The genetic identities of intracellular dinoflagellates (Symbiodinium spp.) in these samples were analyzed using PCR-denaturing gradient gel electrophoresis fingerprinting analysis of the internal transcribed spacer regions 1 and 2. Alcyonaceans from the GBR exhibited a high level of symbiont specificity for Symbiodinium types mostly in clade C. A rare clade D type (D3) was associated only with Clavularia koellikeri, while Nephthea sp. hosted symbionts in clade B (B1n and B36). Homogenous Symbiodinium clade populations were detected in all but one colony. Colonies that appeared bleached possessed symbiont types that were genetically indistinguishable from those in nonbleached conspecifics. These data suggest that parameters other than the resident endosymbionts such as host identity and colony acclimatization are important in determining bleaching susceptibility among soft corals.