Understanding the natural state of coral reefs is paramount to evaluate the response of these ecosystems to local and global human impacts as well as management and conservation strategies. In French Polynesia, some islands are still pristine or uninhabited, such as Tupai atoll. Tupai has been uninhabited, with access to the lagoon prohibited since 2010. However, fishers from nearby islands often take from the outer reef slope at Tupai. Our marine biodiversity survey (coral, macro-invertebrates, and fish) conducted in 2019 highlighted a low density of commercial fish species and top-predators on the outer slope in comparison to the lagoon, where the top-predators represented 16% (of the density) of functional trophic groups. Our surveys also showed a high living coral cover (46%) on the outer slope of Tupai, perhaps due to the absence of both touristic sub-aquatic activities and local pollution from private and commercial activities. Overall, this initial scientific assessment of Tupai has granted an understanding of the spatial patterns of coral, macro-invertebrates, and fish assemblages in the absence of human impacts (i.e., in the lagoon), representing an ecological baseline that could inform conservation management strategies to ensure the preservation of coral reef ecosystem.