We chose a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome, to characterize 60 coral colonies collected during the Tara Pacific expedition and processed in situ, onboard the research vessel Tara. We used Oxford Nanopore Technologies (ONT) to sequence marker gene amplicons. We re-sequenced the same PCR amplicons using Illumina technologies to test the accuracy of Nanopore technology.