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The genetic composition of the resident  Symbiodinium  endosymbionts can strongly modulate the physiological performance of reef-building corals. Here, we used quantitative metabarcoding to investigate  Symbiodinium  genetic diversity in two species of mountainous star corals,  Orbicella franksi  and  Orbicella faveolata , from two reefs separated by 19 km of deep water. We aimed to determine if the frequency of different symbiont genotypes varied with respect to coral host species or geographic location. Our results demonstrate that across the two reefs both coral species contained seven haplotypes of  Symbiodinium , all identifiable as clade B and most closely related to type B1. Five of these haplotypes have not been previously described and may be endemic to the Flower Garden Banks. No significant differences in symbiont composition were detected between the two coral species. However, significant quantitative differences were detected between the east and west banks for three background haplotypes comprising 0.1%–10% of the total. The quantitative metabarcoding approach described here can help to sensitively characterize cryptic genetic diversity of  Symbiodinium  and potentially contribute to the understanding of physiological variations among coral populations.

Quantifying crypticSymbiodiniumdiversity withinOrbicella faveolataandOrbicella franksiat the Flower Garden Banks, Gulf of Mexico