These data consist of sample collection locations and conditions only, not the results of sequencing. These data were an initial collection of an expected time series which was not repeated. Clade data derived from the sample collection described here are archived on GeoSymbio. https://sites.google.com/site/geosymbio/home Coral are symbiotic with photosynthetic dinoflagellates from the genus Symbiodinium. There are eight divergent clades (A-H) within the genus which each contain many genetic varieties. Different types of Symbiodinium have been shown to affect the growth rate and thermal tolerance of the coral. The diversity and population structure of Symbiodinium on a reef and how it changes over time is therefore critical to the stability and resilience of coral reefs. Our research conducted through the MCR LTER project aims at defining the population structure of Symbiodinium present in the corals of Moorea and documenting changes over time.