In 2012 we conducted an integrated ecological assessment of the marine environment of the Pitcairn Islands, which are four of the most remote islands in the world. The islands and atolls (Ducie, Henderson, Oeno, and Pitcairn) are situated in the central South Pacific, halfway between New Zealand and South America. We surveyed algae, corals, mobile invertebrates, and fishes at 97 sites between 5 and 30 m depth, and found 51 new records for algae, 23 for corals, and 15 for fishes. The structure of the ecological communities was correlated with age, isolation, and geomorphology of the four islands. Coral and algal assemblages were significantly different among islands with Ducie having the highest coral cover (56%) and Pitcairn dominated by erect macroalgae (42%). Fish biomass was dominated by top predators at Ducie (62% of total fish biomass) and at Henderson (35%). Herbivorous fishes dominated at Pitcairn, while Oeno showed a balanced fish trophic structure. We found high levels of regional endemism in the fish assemblages across the islands (45%), with the highest level observed at Ducie (56% by number). We conducted the first surveys of the deep habitats around the Pitcairn Islands using drop-cameras at 21 sites from depths of 78 to 1,585 m. We observed 57 fish species from the drop-cams, including rare species such as the false catshark (Pseudotriakis microdon) and several new undescribed species. In addition, we made observations of typically shallow reef sharks and other reef fishes at depths down to 300 m. Our findings highlight the uniqueness and high biodiversity value of the Pitcairn Islands as one of the least impacted in the Pacific, and suggest the need for immediate protection.