Historically, staghorn coral, Acropora cervicornis, was one of the most important reef-building corals in the Caribbean, building extensive thickets at 5-20 m depth that supported diverse ecosystems while providing coastal populations with food, storm protection, and income from tourism. In recent decades, this coral has declined over much of its range, dropping by as much as 97 percent in some localities. To stem its decline, widespread efforts are underway to characterize the physiological and genetic diversity of persisting populations with the goal to restore them to historical levels by out-planting nursery-grown specimens. To support this effort, we sequenced the transcriptome, i.e., the portion of the genome expressed as RNA, for two populations located in Turneffe Atoll Marine Reserve, Belize. These populations experience different temperatures, light levels and water currents, and they harbor individuals that differ in their physiology.