The lack of independently verifiable estimates of catches and fisheries independent estimates of abundance and fishing mortality are major sources of uncertainty in the management of many fisheries. DNA profiling provides the potential to substantially improve the quality of data for assessments and act as an additional deterrent to illegal, unreported, and unregulated (IUU) fishing. Barriers to the implementation of this technology include cost of sample collection and processing, forensic grade quality control, and the ability to apply undetectable tags. We present the results of a comparison of two current and one new (gene tag tool, GTT) sampling techniques, using the highly valued southern bluefin tuna as an example. We demonstrate that fish sampled with two techniques are highly unlikely to be recognised as tagged', whereas one technique was easily recognisable after 73 days. The GTT reduced handling before DNA extraction, whereas both other techniques require additional labour, adding to cost and potential contamination of the evidentiary chain. Evidence of cross-contamination in the Whatman FTA Elute samples suggests they may not be as suitable for at-sea field applications. Two of the three sampling techniques are capable of obtaining high quality tissue samples for stock assessment and chain of custody purposes in a cost-effective and unidentifiable manner.