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Mesophotic ecosystems can harbor a number of unique biological communities and are important for global biodiversity. This research has utilised remote sensing techniques to quantify the communities present in these ecosystems in the Ningaloo Marine Park. Machine learning techniques were used to identify the biotic and abiotic variables that influence the spatial distribution of the habitats and associated biological communities. Subsequent maps have been produced which provide essential information to managers to assess the location, extent, and condition of different marine habitats. This work provides a foundation to further investigate more detailed ecological processes in these ecosystems.