Understanding genetic mechanisms that drive species divergence remains a fundamental question in biology. Coral reefs are among the most diverse systems and recent advances in sequencing technologies have identified widespread cryptic diversity among coral species, some of which has been attributed to reproductive barriers brought on by the timing of spawning. In Western Australia, there are two annual spawning events in autumn and spring. While some species participate in both events, certain species have conspecific colonies that spawn in a genetically predetermined season. In this study, we investigated the genetic and physiological differences between colonies of Acropora tenuis belonging to the spring and autumn lineage. Using whole genome sequencing and transcriptomics, we explored genome-wide patterns of divergence between the two lineages from multiple reef systems and latitudes. We report on the ongoing case of allochronic speciation in a Western Australian coral, seeking to develop a deeper understanding of the mechanisms that underlie this divergence, particularly in the context of climate change and warming summer temperatures.