Sample fragments of three coral species (Acropora pulchra, Pocillopora tuahiniensis, and Porites evermanni) were collected from the lagoon backreef in Moorea, French Polynesia on March 5, 2020 on the north shore. Small RNA sequencing libraries were prepared using NEB Small RNA Library Prep Kit (NEB CAT: E7560S) following the manufacturer's instructions. These reads were used to analyze piRNAs and miRNAs.