We describe the application of the deep learning computerized methodology to the recognition of corals in a shallow reef in the Gulf of Eilat, Red Sea. This project aimed at applying deep neural network analysis, based on thousands of underwater images, to the automatic recognition of some common species among the 100 species reported to be found in the Eilat coral reefs. This is a challenging task, since even in the same colony, corals exhibit significant within-species morphological variability, i.e., age, depth, current, light, geographic location, and inter-specific competition. Since deep learning procedures are based on photographic images, the task is further challenged by image quality, distance from the object, angle of view, and light conditions. We produced a large dataset of over 5000 coral images that were classified into eleven species used in the present deep learning machine classification. We demonstrate the efficiency and reliability of the method, as compared to painstaking manual classification. We demonstrated that this method is readily adaptable to include additional species, providing an excellent tool for the benefit of future studies done in the region, allowing real time monitoring the detrimental effects of global climate change and anthropogenic impacts on the coral reefs of the Gulf of Eilat and elsewhere, and assessing the success of bioremediation efforts.