Threat analyses of the Boraginales were conducted and used to assess the effectiveness of Madagascar’s current and proposed protected area systems in conserving the threatened species of a group of plants widespread in Madagascar. Specimen locality data for 52 species of four families of Boraginales were analysed to provisionally assign species to IUCN Red List categories. Six species were excluded from these global analyses as they are non-native and introduced. IUCN’s criterion B, analysis of geographical range, was found to be the most reliable means of estimating threat, and predicted future decline was found to overestimate threat. Twenty-six of the 46 native species of Boraginales were found to be threatened. Sixty-five percent of these have portions of their ranges in the 2002 protected areas system. When the protected areas system was expanded in 2006 the percentage of species with some protected populations increased to 78%. More than 93% would be protected if a series of proposed priority areas for plant conservation were protected. The implications of these analyses for the conservation of plant species in Madagascar are discussed.