Tetrodotoxin (TTX) is a potent neurotoxin that acts by selectively targeting sodium channels, blocking propagation of action potentials and causing paralysis. It has been responsible for countless human intoxications and deaths around the world, particularly in Japan, from consumption of pufferfish. The distribution of TTX and its analogues is remarkably diverse, and the toxin has been detected in organisms from marine, freshwater and terrestrial environments. Increasing detections of TTX in aquaculture species not typically associated with TTX, such as edible bivalves and gastropods, has drawn considerable attention to the toxin, reinvigorating scientific interest and regulatory concerns. There have been reports of TTX in 18 species of edible shellfish species from ten countries since the 1980’s, with some reports above the safe threshold established by the European Food Safety Authority (EFSA) of 44 μg of TTX per kg of shellfish. Despite decades of research, the exact origin of TTX remains a mystery. Current literature supports three hypotheses: endogenous production, symbiotic bacteria, or direct bioaccumulation through a dietary source. In 2009, the sea slug Pleurobranchaea maculata was found to contain high concentrations of TTX in New Zealand and an extensive research programme to explore the origin of TTX in P. maculata in New Zealand was launched. During this research, Paphies australis, an endemic clam, was found to accumulate high concentrations of TTX (800 μg kg⁻¹). The aim of this thesis was to elucidate the source of TTX in these clams that are a common food source and are culturally important in New Zealand. Paphies australis are largely sessile and found in subtidal habitats making them a highly amedable organisms to investigate the source of TTX. In this thesis, I used a multiple line of evidence approach to investigate potential TTX producers. This included histological and analytical techniques to explore the micro-distribution of TTX within the organs of P. australis, aquaria studies to investigate the depuration and uptake of TTX, field studies to explore the variations in TTX concentrations from different P. australis populations and other bivalve species in New Zealand, and molecular analyses. Immunohistological analysis of P. australis tissues employing a TTX monoclonal antibody demonstrated that TTX was present in the outer cells of the siphons, but also in their digestive system, foot and gill tissues. These results were also supported by chemical analysis using liquid chromatography with tandem mass spectrometry. Observing TTX in organs involved in feeding provided initial evidence to support the hypotheses of an exogenous source in P. australis and presence in siphon tips supports the hypothesis that TTX is used as a chemical defence against predators. The TTX depuration rate in P. australis was then assessed by maintaining TTX-bearing individuals in captivity and feeding them a non-toxic diet for 150 days. The bivalves significantly depurated the toxin (0.4% of total toxin content per day) and there was a rapid decline of the toxin in their digestive glands with only traces amounts remaining after 21 days. This result provides evidence to support the hypothesis that P. australis do not endogenously produce TTX. During field surveys, P. australis from 10 different sites around New Zealand were harvested and tested for TTX. There were significant differences in TTX concentrations from the different sites. All P. australis contained TTX but bivalves from the warmer North Island sites contained significantly higher concentrations than those from the South Island. These results provided further evidence to support the proposition that the source of TTX in P. australis is likely exogenous, varying in abundance by location. I hypothesised that the source is a warm-water-adapted TTX producer that is mostly present or more prevalent in warmer climates, or that TTX production is triggered by warmer temperatures. To explore this possibility further, I used metabarcoding to investigate the bacteria present in the digestive glands and siphons of P. australis from the 10 sites with different TTX concentrations and collected monthly over a year from one site with high TTX concentrations. Marine cyanobacteria, in particular picocyanobacteria (e.g., Cyanobium, Synechococcus, Pleurocapsa, and Prochlorococcus), were found in all samples collected from sites containing the highest amount of TTX and were present in the core microbiome of TTX-bearing P. australis. Cyanobacteria are well known for producing a wide range of marine and freshwater toxins and this finding warrants further investigation. Lastly, I assessed if wild P. australis could sequester and accumulate TTX from a dietary source. I developed a novel method to artificially feed a controlled amount of TTX to bivalves. The micro-encapsulation method incorporated humic acid so that the water-soluble TTX bound to a solid substance. The main finding from this study was that P. australis can rapidly accumulate of TTX from an external dietary source and concentrations were much higher (> 100 μg kg⁻¹) than the safe threshold in bivalves established by the EFSA (44 μg kg⁻¹) in under two weeks. This further strengthens the hypothesis that bivalves most likely accumulate TTX from their diet. This thesis has addressed several critical knowledge gaps in our understanding of the source of TTX in bivalves, particularly in the clam P. australis. A detailed account of each study is presented in this thesis and future research to elucidate the origin of TTX in bivalves are suggested.