Mutualistic dinoflagellate endosymbionts of the genus Symbiodinium are prevalent in marine metazoa and exhibit considerable genotypic and phenotypic plasticity, and variation in biogeographical and ecological distribution. Symbiodinium taxonomy is poorly resolved, but eight lineages have been proposed, based upon sequence variation of nuclear-encoded ribosomal DNA. Three of these clades occur in Caribbean alcyonaceans, yet the diversity of Symbiodinium within these hosts in Bermuda, the northerly limit of their range, is unknown. Using large sub-unit and internal transcribed spacer regions of rDNA, this study shows that clade B, a diverse symbiont assemblage, is the only genotype found in alcyonacean hosts in Bermuda. Some conspecific hosts from the Caribbean additionally harbor clade C, yet diversity at the subcladal level, as indicated by ITS data, is comparable between both regions. Some host specificity was observed and host identity, as opposed to environmental correlates, appears to be the most important factor governing alcyonacean-Symbiodinium symbioses.