Four new species of Coenogonium are described from the Caribbean island of Puerto Rico—C. aurantiacum Mercado-Díaz & Lücking, C. borinquense Mercado-Díaz & Lücking, C. dimorphicum Mercado-Díaz & Lücking and C. portoricense Mercado-Díaz & Lücking. All were discovered in small and highly fragmented forest remnants of relatively rare Puerto Rican forest ecosystems, Pterocarpus wetlands and non-calcareous dry forests. The discoveries are discussed relative to the conservation status of these threatened ecosystems, the need to catalogue biodiversity before it vanishes, and the notion that endemism in lichenized fungi in island biotas is potentially much higher than hitherto assumed. A previous world-wide key to Coenogonium is updated to accommodate the new taxa.