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Ribosomal DNA sequence data abounds from numerous studies on the dinoflagellate endosymbionts of corals, and yet the multi-copy nature and intragenomic variability of rRNA genes and spacers confound interpretations of symbiont diversity and ecology. Making consistent sense of extensive sequence variation in a meaningful ecological and evolutionary context would benefit from the application of additional genetic markers. Sequences of the non-coding region of the plastid psbA minicircle ( psbA ncr  ) were used to independently examine symbiont genotypic and species diversity found within and between colonies of Hawaiian reef corals in the genus  Montipora . A single  psbA ncr   haplotype was recovered in most samples through direct sequencing (∼80–90%) and members of the same internal transcribed spacer region 2 ( ITS2 ) type were phylogenetically differentiated from other  ITS2  types by substantial  psbA ncr   sequence divergence. The repeated sequencing of bacterially-cloned fragments of  psbA ncr   from samples and clonal cultures often recovered a single numerically common haplotype accompanied by rare, highly-similar, sequence variants. When sequence artifacts of cloning and intragenomic variation are factored out, these data indicate that most colonies harbored one dominant  Symbiodinium  genotype. The cloning and sequencing of  ITS2  DNA amplified from these same samples recovered numerically abundant variants (that are diagnostic of distinct  Symbiodinium  lineages), but also generated a large amount of sequences comprising PCR/cloning artifacts combined with ancestral and/or rare variants that, if incorporated into phylogenetic reconstructions, confound how small sequence differences are interpreted. Finally,  psbA ncr   sequence data from a broad sampling of  Symbiodinium  diversity obtained from various corals throughout the Indo-Pacific were concordant with  ITS  lineage membership (defined by denaturing gradient gel electrophoresis screening), yet exhibited substantially greater sequence divergence and revealed strong phylogeographic structure corresponding to major biogeographic provinces. The detailed genetic resolution provided by  psbA ncr   data brings further clarity to the ecology, evolution, and systematics of symbiotic dinoflagellates.

Improved Resolution of Reef-Coral Endosymbiont (Symbiodinium) Species Diversity, Ecology, and Evolution through psbA Non-Coding Region Genotyping