The diversity of endosymbiotic dinoflagellates (Symbiodinium) in corals at Johnston Atoll in the central Pacific Ocean was assessed using both the internal transcribed spacer 2 (ITS2) region of the nuclear rDNA and chloroplast 23S rDNA. More sequences were recovered from corals using the ITS2 primers than with the chloroplast 23S primers, a finding that reflects both the higher taxonomic resolution and level of intragenomic variation in ITS2 in eukaryotes as compared to chloroplast 23S. Parsimony network analysis, Bray-Curtis coefficient of similarity and 1-way analysis of similarity resolved coral species- and/or genus-specific lineages and/or groupings of Symbiodinium that were generally congruent between the 2 genetic markers. Comparison of coral-Symbiodinium assemblages at Johnston Atoll with those in corals sampled on other reefs in the Pacific reveals differences that include novel host-symbiont unions and a Symbiodinium lineage previously reported to be Caribbean-specific in Acropora from Johnston Atoll.