Giant clams (conventionally family Tridacnidae) are a conspicuous inhabitant of coral reefs throughout the Indo-Pacific region. Surprisingly, anecdotal reports, and museum voucher specimens, suggest that the fluted giant clam Tridacna squamosa may be species of giant clam inhabiting rocky coral reefs in the Northern Territory (NT), despite a possible 10 being known from the Indo-Pacific. Our research is the first to investigate the abundance, distribution, and phylogeography of giant clams within the coastal reefs of the NT. The NT is a sparsely populated area of northern Australia, with limited infrastructure in the mostly remote coastline. Travel relies on planes or boats, subject to prevailing weather conditions. In these circumstances, underwater survey using SCUBA is an expensive and time consuming exercise, carrying a significant risk of attack from sharks and estuarine crocodiles. We developed a novel underwater video system to survey reefs in three remote regions of Arnhem Land, NT. Using a commercially available GPS, depth sounder, video lens, and text overlay box we built a relatively cheap, portable and easy to use georeferenced video system to survey reefs in shallow water. The equipment was tested and calibrated before it was used in the field. After each survey, image frames were extracted from the video transects and calibrated before virtual quadrats were overlaid and measurements taken. Multivarate analysis was used to compare the percentage of habitat coverage within sites with and without clams, and between sites, areas and regions. Length frequency was estimated from calibrated video frames, and abundance from transect observations.