Sequencing of prokaryotic 16S rRNA (V3V4 multivariable region) from four Montipora capitata coral colonies collected in Kaneohe Bay, Hawaii, that were exposed to thermal stress. Over a five-week period, the coral nubbins collected from the four colonies were exposed to ambient and thermal stress conditions, with sequencing of bacterial 16S rRNA performed at three key time points designed to capture the response of the corals to bleaching. Additionally, nubbins from each wild colony were flash frozen directly from the field.