Here we provide the raw transcriptomes of Acropora hyacinthus corals that were exposed to experimental acute high heat stress and then monitored for four months throughout their heat stress recovery in a common garden reef environment. All corals were collected from Double Reef (2 adjacent shallow patch reef environments) in Palau's southern lagoon.</p><p>This study's main goal was to evaluate whether corals with different heat stress resistance levels exhibit different heat stress recovery abilities following bleaching. We investigated this by exposing Acropora hyacinthus corals of different heat resistance ability to high heat stress until reaching approximately 50% pigmentation loss (i.e., moderate bleaching), which meant heating each individual coral colony for however many days necessary to achieve the bleaching target. We then divided corals into 3 main bleaching resistance groups based on the number of days to achieve bleaching: low resistance (4 days, 9 colonies), moderate resistance (5-6 days, 9 colonies), and high resistance (7-9 days, 9 colonies). There were also 12 colonies whereby heated or control ramets died during the heat stress experiment and were not included in the downstream recovery experiment. After heat stress, surviving bleached colonies (and non-stressed controls for each colony) were deployed back onto Double Reef in a common garden recovery experiment for 4 months. In total, we extracted RNA for transcriptomes from all surviving colonies at the following timepoints: pre heat stress, ~16 hours post heat stress, ~2 weeks post heat stress, ~1 month post heat stress, and ~4 months post heat stress.