The aim of my PhD research is to investigate the mesophotic communities in the Ningaloo Marine Park to gain an understanding of the communities present, their distribution and their linkages to shallow water areas. Mesophotic coral ecosystems (MCEs) are defined as light-dependent communities occurring from approximately 30m to the bottom of the photic zone. Due to their location MCEs are a relatively understudied class of ecosystem. However, they have started to attract increased research attention following recent technological developments. These areas are thought to act as continuations of the shallow reef communities above, where a diverse range of taxa has been observed. The Ningaloo Park, in particular, is famed for high biodiversity, yet the deeper water areas that make up a majority of the park remain relatively unstudied. My work involves using a number of remote sensing methods including Autonomous Underwater Vehicles (AUVs) and Multibeam Acoustics to produce benthic substratum maps and community distribution models of these deeper areas.