1984: The idea for the CARRUS Alliance stems to a meeting held in Belize more than 30 years ago, in which approximately 40 coral reef scientists determined that the most rational approach to understand whole reef systems was to do so via coordinated long-term studies of reef systems in various parts of the world based on common research objectives, including the development of ecological models. It was realized at the time that it would be unrealistic to fund a large number of such studies from a single source. The original plan to initiate the work on two comparative sites was not funded.

1992: In 1992, a meeting of about 50 researchers during the 7^th International Coral Reef Symposium in Guam concluded that an understanding of the impacts of climate change on coral reefs would be best attained through coordinated long-term studies of a large number of coral reefs around the world, to be conducted by research institutions. Following this meeting, there was no funding to fully develop such a network.

2001: Long-term, large-scale comparative research was identified as a Caribbean regional priority in the 2001 international workshop “Caribbean Coral Reef Research Priorities”, hosted by NCORE, sponsored by EPA and the Khaled bin Sultan Living Oceans Foundation, and involving participants from 11 countries. It thus became an institutional priority for NCORE to find a way to facilitate the development of this research approach. It was determined that acquiring funding for setting up a reasonable number of new large-scale projects was not feasible. However, by this time, many large-scale coral reef studies had already been initiated around the world. The goal was then set at forming an alliance to facilitate the development of convergent research goals among existing whole-reef studies. One potential common goal was the development of GIS-based Decision Support Tools, which would incorporate as much scenario-testing capability as possible. One particularly promising approach under development was agent-based modeling, which could incorporate both human and ecological aspects of coral reef management within a GIS framework. This, and other modeling and decision support approaches were discussed in a second international Conference/Workshop  "The Future of Decision Support for Coral Reef Management: Agent-Based Models and Long-term Ecological Research". Recommendations for initial development of these approaches have provided a basis for some of the subsequent research of NCORE.

2004: The Alliance was officially announced in 30 June 2004 during the 10th International Coral Reef Symposium (ICRS) in Okinawa, Japan.