The benthic invertebrate, plant and fish biodiversity of the 50,000 km² area of the Torres Strait Protected Zone and adjacent shelf seabed was sampled by a 200 m tow of a 1.5 m epibenthic sled at 166 sites, representing a wide range of known physical environments, during one 1-month-long voyage on the James Cook University vessel James Kirby. More than 1,550 species/species-equivalent OTUs (operational taxonomic units) were identified. The dataset comprises 8,569 site-by-species records. A pipe-dredge was attached to the sled to collect sediment samples: a 500 ml subsample was processed for particle size and carbonate by Geoscience Australia; another 500 ml subsample was sieved on 1 mm mesh and preserved in 10% Formalin - Rose Bengal solution.