Background: The coral holobiont is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with a yet undefined large number of symbiotic eukaryotes, bacteria and viruses. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring. <p> Methods & Principal Findings: We investigated the diversity of eukaryotic community associated with a common reef-building coral species from the southern Great Barrier Reef, Australia. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene assays to demonstrate the presence of the “type-N” (cf. Gemmocystis cylindrus) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) in all examined coral and a photosynthetic sister species to Apicomplexa - Chromera velia - in Montipora digitata. Eukaryotic small-subunit rRNA gene clone library confirmed presence of Symbiodinium sp. Clade C corroborating findings using amplicon pyrosequencing and diagnostic PCR confirmed presence of apicomplexan type-N. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus) in M. digitata DNA. We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively. <p> Significance: This study proved that eukaryote tag encoded amplicon pyrosequencing is capable of demonstrating presence of C. velia and apicomplexan type-N in total coral DNA. This is the first time apicomplexan type-N has been observed in the Great Barrier Reef. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease.