Studies on coral reefs increasingly combine aspects of science and technology to understand the complex dynamics and processes that shape these benthic ecosystems. Recently, the use of advanced computational algorithms has entered coral reefs science as new powerful tools that help solve complex coral reef related questions, which were unsolvable just a decade earlier. Some of these advanced algorithms consist of Computational Intelligence (CI) approaches, a branch of Artificial Intelligence that uses intelligent systems to address complex real-world problems yielding more robust, tractable and simpler solutions than those obtained by conventional mathematical techniques. This paper describes the most commonly used CI techniques related to coral reefs and the main improvements obtained with these methods over classical algorithms in this field. Some recommendations are given for the application of CI techniques to complex coral reef related problems, and vice-versa, for the application of novel coral reef dynamics concepts to improve the Coral Reefs Optimization (CRO) algorithm, an optimization method inspired by coral reef dynamics.