Sea cucumbers are conspicuous members of coral reef communities and serve numerous ecological functions such as sediment aeration and nutrient cycling. Thus, a decline in sea cucumber populations will have a detrimental effect on the coral reef ecosystem. Australia’s Great Barrier Reef supports a diversity of commercially important sea cucumber species and understanding their habitat preference is critical for conservation and development of sustainable fishery management strategies as well as enhancing our knowledge of their ecology. Traditionally, habitat preference of echinoderms is determined by population counts using transects and these counts are correlated with associated habitat. However, these approaches do not account for surrounding habitat or the complexity of overlapping habitats on the coral reef. In this study we utilised photogrammetry to construct twenty, 25-metre diameter orthomosaics of the reef containing a range of sea cucumbers and habitat to assess habitat preference of the CITES listed black teatfish Holothuria whitmaei and their relationship with conspecifics and other species. Habitat metrics are classified in terms of the habitat type, rugosity, slope and interspecies interactions. The results from this study provide a clear picture of which habitats H. whitmaei prefer and highlight the advantages of underwater photogrammetry.