The need for rapid methodologies for measuring coral reef resilience and their application in assessing the effectiveness of coral reef conservation management measures is becoming increasingly acute, especially in the developing world. It is therefore crucial to develop monitoring and assessment protocols to build an understanding of bleaching resistance and resilience indicators for application in management, and to determine how MPA management actions can influence resilience and resistance. This protocol is one attempt at defining some basic resilience indicators that can be quantified using rapid assessment methods.