Abstract Many reef‐building tropical corals are becoming rare. We considered the meaning of rarity in corals and highlighted taxa that have reached low abundances in the last few decades. The difficulties of quantifying rarity in the marine environment arise from the sheer scale and 3‐dimensional nature of the biome and the inherent challenges therein of ecological surveys with scuba. To meet the demands of coral conservation biology in the 21st century, we suggest that contemporary studies of coral communities will require enhanced capacity to identify species and a species‐specific focus on corals occurring at low abundances, which traditional ecological approaches to quantifying populations of benthic marine organisms have a limited capacity to address. Now is the time to revise scientific approaches to respond to the challenges posed by the need to understand and protect rare tropical corals.