Stony (scleractinian) corals are common on seamounts and can form extensive reef-like structures which in turn provide important habitat for associated species. Aggregations of fish also occur on seamounts, which in recent decades have become the target of commercial bottom trawl fisheries that have damaging impacts on benthic communities. Such fisheries occur throughout the world’s oceans, and the majority are located on seamounts about which little is known of their biodiversity or likely fisheries impact. Here we develop an index of risk for stony corals on seamount summits. The index combines a metric of vulnerability measured by the coincidence of seamount summits, target fish ranges and likelihood of coral presence with an assessment of likely fisheries impact derived from a fishing intensity effects study and fishing effort-catch data. We provide spatial maps depicting the locations of vulnerable seamount features, and those at particular risk to bottom trawling. Application of the risk index may help to provide guidance to fisheries or environmental managers faced with balancing fisheries management and habitat conservation.