Corals on the world’s warmest reefs in the Arabian/Persian Gulf tolerate have high thermal tolerance relative to corals living in typical reef environments. This unusual thermal tolerance may provide insights into the mechanisms and limits for corals’ adaptation to warming oceans. To develop the brain coral Platygyra daedalea as a model for studying this thermal tolerance, we’ve constructed a genetic linkage map using multilocus SNP genotypes from individual larvae. This resource will enable genomic studies of trait associations and population divergence, making it possible to identify genomic regions associated with the unusually high thermal tolerance of these populations.