The taxonomic diversity of endosymbiont Symbiodinium species and the physiological contributions they confer to coral host species are challenging to assess. It seems likely the genetic diversity of obligate Symbiodinium species modulates the physiological performance of reef building corals. Here we used deep amplicon sequencing to reveal high genetic diversity of the endosymbiotic dinoflagellate, Symbiodinium, in coral hosts by amplifying ribosomal DNA internal transcribed spacer region 2 (ITS-2). We revealed quantitative proportions of mixed Symbiodinium populations within the Orbicella species complex collected from three Caribbean locations. Symbiodinium diversity at the Flower Garden Banks for Orbicella franksi and Orbicella faveolata demonstrated coral host species contained Symbiodinium clade B type B1 and detected five genetically variable B1 Symbiodinium types, three of which may be endemic to the Flower Garden Banks locations. Our second dataset assessed Symbiodinium diversity in O. faveolata collected from Puerto Morelos, Mexico, previously genotyped using restriction fragment length polymorphism (RFLP) and direct sequencing. We detected an additional background population of clade A, type A13. Additionally we showed one colony hosted a mixed infection of Symbiodinium genotypes B1 and A13 where RFLP and direct sequencing assigned genotypes C7 and B1. Our third dataset assessed Symbiodinium diversity across a depth gradient in O. faveolata collected from Curaçao using the Illumina MiSeq platform. We showed shallow water coral hosted a more complex mixed infection relative to hosts from deeper waters and detected Symbiodinium genotype G3, a genotype not commonly associated with scleractinian hosts. These results highlight the need for consistent molecular genotyping techniques to assess community assemblages of Symbiodinium-host relationships. This deep sequencing approach used to characterize cryptic genetic diversity of Symbiodinium will potentially contribute to the understanding of physiological variations among coral populations.