Coral reefs face increased environmental threats from anthropomorphic climate change and pollution, from agriculture, industries and tourism. They are economically vital for many people worldwide, and harbour a fantastically diverse ecosystem, being the home for many species of fish and algae. Surprisingly little is known about the microbial communities living in and in the surrounding of coral reefs. The objectives of this project is to characterise the community composition and function of bacteria living in the water and the upper sediment layer in close proximity of coral reefs. In this project we sequenced 3 water samples and 3 sediment samples out of the coast of Kenya, at 3 distinct location: Mombasa, Malindi and Kisite.